Supplemental Figure S1. DSB repair assays and generation...

40

Transcript of Supplemental Figure S1. DSB repair assays and generation...

Page 1: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 2: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S1. DSB repair assays and generation of a stable U2OS GFP-RPB1 cell line (A) Western blot analysis of XRCC4 and WWP2 expression in cells from Fig. 1A. Tubulin is

a loading control.

(B) Schematic representation of the EJ5-GFP reporter for NHEJ.

(C) Western blot analysis of WWP2 expression in cells from Fig. 1B. Tubulin is a loading

control.

(D) Schematic representation of the plasmid integration assay.

(E) Western blot analysis of WWP2, RPB1 and p-RPB1 (S2) expression in U2OS and stable

U2OS GFP-RPB1 cells. Tubulin is a loading control. Relative expression levels of the

indicated proteins in U2OS GFP-RPB1 versus U2OS cells (set to 1) following correction for

loading based on tubulin levels is indicated below the blots.

(F) Representative microscopy images showing nuclear localization of GFP-RPB1.

Page 3: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 4: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S2. WWP2 is recruited to sites of damage and promotes DNA repair (A) Western blot analysis of the indicated proteins in U2OS cells transfected with the

indicated siRNAs. Tubulin is a loading control.

(B) Schematic of the HA-ER-I-PpoI system in U2OS cells used to generate site-specific

DSBs at the indicated genes following 4-hydroxytamoxifen (4-OHT) treatment. Blue boxes

indicate positions of primers used to monitor protein binding by ChIP-qPCR. Green boxes

indicate positions of primers used to quantify mRNA levels of the indicated genes by RT-

qPCR. Red boxes indicate positions of primers used to measure the cleavage efficiency of I-

PpoI.

(C) ChIP-qPCR against WWP2 in U2OS HA-ER-I-PpoI cells at the indicated time points after

(4-OHT) treatment and at the indicated positions at DAB1 and SLCO5a1. The mean ±SD

from qPCR replicates of one experiment is shown. This is a repeat of the experiment shown

in Fig. 2D.

(D) Same as in D, except that WWP2 levels were monitored at INTS4 and p21.

(E) Cutting efficiency at RYR2 at the indicated time points after (4-OHT) treatment in U2OS

HA-ER-I-PpoI cells transfected with the indicated siRNAs. The mean ±SD from qPCR

replicates of a representative experiment is shown. A repeat of the experiment is shown in

Supplemental Fig. S8A.

(F) Western blot analysis of WWP2 expression in cells from Fig. 2E. Tubulin is a loading

control.

(G) ChIP-qPCR against gH2AX in U2OS HA-ER-I-PpoI cells at the indicated time points after

(4-OHT) treatment and at the indicated positions at DAB1 and SLCO5a1. The mean ±SD

from qPCR replicates of one experiment is shown. A repeat of the experiment shown in

Supplemental Fig. S9.

(H) As in G, except that gH2AX levels were monitored at INTS4 and p21.

Page 5: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 6: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S3. WWP2 promotes DSB-induced transcription silencing and RPB1 is ubiquitylated after DNA damage

(A) RT-qPCR analysis of RYR2 expression levels in U2OS ER-I-PpoI cells at the indicated

timepoints after (4-OHT) treatment and transfected with the indicated siRNAs. RYR2 mRNA

levels are normalized to those of cyclophilin B. The mean ±SD from qPCR replicates of a

representative experiment is shown. A repeat of the experiment is shown in Supplemental

Fig. S8B.

(B) Schematic of the assay used to monitor nascent transcription by 5-ethynyl uridine (5-EU)

incorporation at DNA damage sites induced by UV-A laser micro-irradiation (upper panel).

(C) UV-A laser-micro-irradiation of U2OS cells transfected with the indicated siRNAs and

analyzed by immunofluorescence following 5-EU and DAPI incorporation. 53BP1 is a DNA

damage marker.

(D) Quantification of nascent transcription in C. Grey dots represent nascent transcription

levels in individual nuclei. Black lines represent the mean nascent transcription level in all

nuclei analyzed per sample.

(E) Pulldowns of GFP GFP-RPB1 under non-denaturing (EBC) and denaturing conditions in

U2OS cells. Blots were probed for RPB2 and GFP.

(F) Pulldowns of GFP-RPB1 under denaturing conditions in untreated and UV-irradiated

U2OS cells. Blots were probed for FK2 (ubiquitin), Ub(K48) and GFP.

(G) Pulldowns of GFP-RPB1 under denaturing conditions in untreated and phleomycin

(Phleo)-, etoposide (Eto)- or doxorubicin (Doxo)-treated U2OS cells. Cells were also treated

with proteasome inhibitor (MG-132) 25 minutes before treatment with DNA damaging

agents. Blots were probed for Ub(K48), FK2 (ubiquitin) and GFP. Tubulin is a loading

control.

(H) Same as in G, except that phleomycin (Phleo) and neocarsinostatin (NCS) were used to

induce DSBs. Blots were probed for Ub(K48), GFP and gH2AX. Tubulin is a loading control.

(I) Pulldown of ubiquitylated proteins by the TUBE approach in U2OS cells stably expressing

GFP-RPB1. Cells were treated with the indicated siRNAs and with proteasome inhibitor

(MG-132) 25 minutes before treatment with DNA damaging agents. Blots were probed for

Ub(K48), GFP, WWP2 and gH2AX. Tubulin is a loading control.

Page 7: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 8: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S4. DNA-PK and WWP2 co-operate to promote DNA damage-induced RPB1 ubiquitylation

(A) Pulldowns of ubiquitylated proteins in U2OS using the TUBE approach. Cells were

treated with a broad-spectrum inhibitor of de-ubiquitylating enzymes (PR169) and the

indicated siRNAs before phleomycin (Phleo) treatment. Blots were probed for p-RPB1 (S2),

gH2AX and H2A.

(B) Western blot analysis of the indicated proteins in U2OS cells from A. Tubulin is a loading

control.

(C) Pulldowns of GFP-RPB1 under denaturing conditions in U2OS cells treated with the

indicated siRNAs. Cells were also treated with proteasome inhibitor (MG-132) 25 minutes

before the phleomycin treatment. Blots were probed for Ub(K48), GFP, gH2AX, H3, Ku80,

LigIV and DNA-PKcs. Tubulin is a loading control.

(D) As in C, except that cells were treated with siRNAs against Luciferase (siLuc) and

WWP2 and that blots were probed for WWP2 instead of Ku80, LigIV and DNA-PKcs.

(E) Immunofluorescence images (upper panel) of Ub(K48) accumulation at DNA damage

tracks generated by multiphoton laser micro-irradiation in U2OS cells that were left untreated

or treated with DNA-PK inhibitor (DNA-PKi). gH2AX is a DNA damage marker. Western blot

analysis (lower panel) of DNA-PK activation 1 hour after 10 Gy of irradiation radiation (IR).

Blots were probed for p-DNA-PKcs (S2056), DNA-PKcs, p-ATM (S1981) and ATM.

(F) Same as in E, except that cells were transfected with the indicated siRNA (upper panel).

Western blot analysis (lower panel) of WWP2 expression levels. Blots were probed for

WWP2. Tubulin is a loading control.

(G) Quantification of upper panels in E (left) and F (right). The mean ±S.E.M from 3

independent experiments is shown. Statistical significance was calculated using the

Student’s t-test (p<0,05 *, p<0,01 **, p<0,001 ***).

Page 9: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 10: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S5. DNA-PK regulates RPB1 levels at broken genes (A) ChIP-qPCR against gH2AX in DMSO-treated (control) and DNA-PKi-treated U2OS HA-

ER-I-PpoI cells at the indicated time points after (4-OHT) treatment and at the indicated

positions at DAB1 and SLCO5a1. The mean ±SD from qPCR replicates of a representative

experiment is shown.

(B) As in A, expect that RPB1 and S2, S5 or S7 phosphorylated (p-)RPB1 were examined at

the OMA1 and PRKAA2 genes. A repeat of the experiment is shown in Supplemental Fig.

S12A-B.

(C) As in A, expect for OMA1 and PRKAA2. A repeat of the experiment is shown in

Supplemental Fig. S12A-B.

(D) Western blot analysis of RPB1 and S2, S5 or S7 phosphorylated (p-)RPB1 levels on

chromatin isolated from DMSO-treated (control) and DNA-PKi-treated U2OS cells at the

indicated time points after treatment with neocarzinostatin (NCS). H4 is a loading control.

gH2AX is a DNA damage marker.

Page 11: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 12: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S6. Proteasome is recruited to broken genes in a DNA-PKcs- and WWP2-dependent manner (A) Western blot analysis of S2, S5 or S7 phosphorylated (p-)RPB1 levels on chromatin

isolated from DMSO-treated (control) and MG-132-treated U2OS cells at the indicated time

points after treatment with neocarzinostatin (NCS). H4 is a loading control. gH2AX is a DNA

damage marker.

(B) ChIP-qPCR against the 19S and 20S proteasome in U2OS HA-ER-I-PpoI cells at the

indicated time points after (4-OHT) treatment at OMA1 and PRKAA2. The mean ±SD from

qPCR replicates of a representative experiment is shown. A repeat of the experiment is

shown in Supplemental Fig. S13C.

(C) Same as in B, except that cells were transfected with the indicated siRNA. A repeat of

the experiment is shown in Supplemental Fig. S14C.

Page 13: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 14: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S7. WWP2 promotes binding of NHEJ factors on damaged chromatin (A) Immunofluorescence images of mCherry-NBS1 recruitment to DNA damage tracks

generated by UV-A laser-micro-irradiation in U2OS cells transfected with the indicated

siRNAs and an mCherry-NBS1 expression vector. The mean ±SD from 3 independent

experiments is shown.

(B) Quantification of A. The mean ±S.E.M from 3 independent experiments is shown.

Statistical significance was calculated using the Student’s t-test (p<0,05 *, p<0,01 **,

p<0,001 ***).

(C) Western blot analysis of WWP2 expression in cells from A. Blots were probed for

WWP2. Tubulin is a loading control.

(D) Western blot analysis of the indicated proteins in soluble and chromatin fractions from

untreated and Phleomycin (Phleo-)treated U2OS cells. Tubulin and H4 are loading controls.

gH2AX is a DNA damage marker. A representative experiment is shown.

(E) Quantifications of Ku70 and XRCC4 levels in D. The mean ±SD from 3 independent

experiments is shown. Statistical significance was calculated using the Student’s t-test

(p<0,05 *, p<0,01 **, p<0,001 ***).

(F) Immunofluorescence images of gH2AX foci formation 1 hour after 10 Gy of IR in U2OS

cells transfected with the indicated siRNAs.

(G) Quantification of F. The mean ±S.E.M from 3 independent experiments is shown.

Statistical significance was calculated using the Student’s t-test (p<0,05 *, p<0,01 **,

p<0,001 ***).

(H) Western blot analysis of WWP2 expression in cells from F. Blots were probed for

WWP2. Tubulin is a loading control.

(I) Pulldown of ubiquitylated proteins using the TUBE approach in NIH3T3 cells stably

expressing wild-type (8K) or mutant (0K) GFP-RPB1. Cells were treated with proteasome

inhibitor (MG-132) 25 minutes before phleomycin treatment. Blots were probed for GFP,

Ub(K48) and gH2AX. Tubulin is a loading control.

(J) Pulldown of GFP from U2OS cells transiently expressing GFP, wild-type (8K) GFP-RPB1

or mutant (0K) GFP-RPB1. Blots were probed for WWP2 and GFP.

Page 15: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 16: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S8. WWP2 promotes DNA repair and transcription arrest at broken genes (A) Repeat of the experiments shown in Fig. 2H and Supplemental Fig. S2E.

(B) Repeat of the experiments shown in Fig. 3A-B and Supplemental Fig. S3A.

(C) Repeat of the experiments shown in Fig. 3C.

(D) Repeat of the experiments shown in Fig. 3D.

(E) Repeat of the experiments shown in Fig. 3E.

Page 17: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 18: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S9. Induction of gH2AX in WWP2-depleted cells (A) Repeat of the experiments shown in Supplemental Fig. 2G.

(B) Repeat of the experiments shown in Supplemental Fig. 2G.

Page 19: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 20: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S10. DNA-PK controls RPB1 levels at broken genes (A) Repeat of the experiments shown in Fig. 4C.

(B) Repeat of the experiments shown in Fig. 4D.

Page 21: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 22: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S11. DNA-PK controls phosphorylated RPB1 levels at broken genes (A) Repeat of the experiments shown in Fig. 4C.

(B) Repeat of the experiments shown in Fig. 4D.

Page 23: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 24: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S12. RPB1 and phosphorylated RPB1 levels remain unaffected at non-damaged genes Repeat of the experiments shown in Supplemental Fig. S5B.

Page 25: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 26: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S13. Proteasome is recruited to broken genes (A) Repeat of the experiments shown in Fig. 5A-B.

(B) Repeat of the experiments shown in Fig. 5C-D.

(C) Repeat of the experiments shown in Supplemental Fig. 6B.

Page 27: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter
Page 28: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Figure S14. Proteasome is recruited to broken genes (A) Repeat of the experiments shown in Fig. 5E-F.

(B) Repeat of the experiments shown in Fig. 5G-H.

(C) Repeat of the experiments shown in Supplemental Fig. S6C.

Page 29: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Supplemental Table S1: Proteins identified as interactors of WWP2 by SILAC LC-MS/MS

Light (L): U2OS-GFPHeavy (H): U2OS-WWP2-GFP

Protein names Gene names Fasta headers Ratio H/LS1 RNA-binding domain-containing protein 1 SRBD1 sp|Q8N5C6-2|SRBD1_HUMAN Isoform 2 of S1 RNA-binding domain-containing protein 1 OS=Homo sapiens GN=SRBD1;sp|Q8N5C6|SRBD1_HUMAN S1 RNA-binding domain-containing protein 1 OS=Homo sapiens GN=SRBD1 PE=1 SV=2;tr|B7Z6X7|B7Z6X7_HUMAN S1 RNA-binding domain-contai47,74RNA-binding protein 14 RBM14 sp|Q96PK6|RBM14_HUMAN RNA-binding protein 14 OS=Homo sapiens GN=RBM14 PE=1 SV=243,47WD repeat-containing protein 92 WDR92;DKFZp434B156sp|Q96MX6|WDR92_HUMAN WD repeat-containing protein 92 OS=Homo sapiens GN=WDR92 PE=1 SV=1;sp|Q96MX6-2|WDR92_HUMAN Isoform 2 of WD repeat-containing protein 92 OS=Homo sapiens GN=WDR92;tr|Q8ND98|Q8ND98_HUMAN Putative uncharacterized protein DKFZp434B156 OS=H42,48DNA-directed RNA polymerase;DNA-directed RNA polymerase II subunit RPB2POLR2B tr|C9J2Y9|C9J2Y9_HUMAN DNA-directed RNA polymerase OS=Homo sapiens GN=POLR2B PE=2 SV=2;sp|P30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 OS=Homo sapiens GN=POLR2B PE=1 SV=1;tr|C9J4M6|C9J4M6_HUMAN DNA-directed RNA polymerase OS=Homo sapiens G42,12DNA-directed RNA polymerase II subunit RPB9POLR2I sp|P36954|RPB9_HUMAN DNA-directed RNA polymerase II subunit RPB9 OS=Homo sapiens GN=POLR2I PE=1 SV=1;tr|K7EK49|K7EK49_HUMAN DNA-directed RNA polymerase II subunit RPB9 OS=Homo sapiens GN=POLR2I PE=2 SV=1;tr|K7EKS1|K7EKS1_HUMAN DNA-directed RNA polymerase I41,55DNA-directed RNA polymerase II subunit RPB3POLR2C sp|P19387|RPB3_HUMAN DNA-directed RNA polymerase II subunit RPB3 OS=Homo sapiens GN=POLR2C PE=1 SV=241,45Heterogeneous nuclear ribonucleoprotein U-like protein 1HNRNPUL1 sp|Q9BUJ2-2|HNRL1_HUMAN Isoform 2 of Heterogeneous nuclear ribonucleoprotein U-like protein 1 OS=Homo sapiens GN=HNRNPUL1;sp|Q9BUJ2|HNRL1_HUMAN Heterogeneous nuclear ribonucleoprotein U-like protein 1 OS=Homo sapiens GN=HNRNPUL1 PE=1 SV=2;tr|B7Z4B8|B7Z4B8_39,08Low-density lipoprotein receptor class A domain-containing protein 4LDLRAD4 tr|K7EN38|K7EN38_HUMAN Low-density lipoprotein receptor class A domain-containing protein 4 OS=Homo sapiens GN=LDLRAD4 PE=2 SV=1;sp|O15165-5|LRAD4_HUMAN Isoform 5 of Low-density lipoprotein receptor class A domain-containing protein 4 OS=Homo sapiens GN=LD38,70DNA-directed RNA polymerase II subunit RPB4POLR2D sp|O15514|RPB4_HUMAN DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens GN=POLR2D PE=1 SV=1;tr|E9PB93|E9PB93_HUMAN DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens GN=POLR2D PE=2 SV=1;tr|E9PHV4|E9PHV4_HUMAN DNA-directed RNA polymerase I38,34Cleavage and polyadenylation specificity factor subunit 7CPSF7 sp|Q8N684-2|CPSF7_HUMAN Isoform 2 of Cleavage and polyadenylation specificity factor subunit 7 OS=Homo sapiens GN=CPSF7;sp|Q8N684|CPSF7_HUMAN Cleavage and polyadenylation specificity factor subunit 7 OS=Homo sapiens GN=CPSF7 PE=1 SV=1;sp|Q8N684-3|CPSF7_HUM37,88NEDD4-like E3 ubiquitin-protein ligase WWP1WWP1 sp|Q9H0M0-6|WWP1_HUMAN Isoform 6 of NEDD4-like E3 ubiquitin-protein ligase WWP1 OS=Homo sapiens GN=WWP1;sp|Q9H0M0-3|WWP1_HUMAN Isoform 3 of NEDD4-like E3 ubiquitin-protein ligase WWP1 OS=Homo sapiens GN=WWP1;sp|Q9H0M0|WWP1_HUMAN NEDD4-like E3 ubiquitin-pro37,0760S ribosomal protein L38 RPL38 sp|P63173|RL38_HUMAN 60S ribosomal protein L38 OS=Homo sapiens GN=RPL38 PE=1 SV=2;tr|J3KT73|J3KT73_HUMAN 60S ribosomal protein L38 OS=Homo sapiens GN=RPL38 PE=2 SV=1;tr|J3QL01|J3QL01_HUMAN 60S ribosomal protein L38 OS=Homo sapiens GN=RPL38 PE=2 SV=1;tr|J3K37,05DNA-directed RNA polymerases I, II, and III subunit RPABC2POLR2F tr|U3KQS8|U3KQS8_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Homo sapiens GN=POLR2F PE=4 SV=1;tr|F8WC47|F8WC47_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Homo sapiens GN=POLR2F PE=2 SV=1;tr|U3KPY1|U3KPY1_HUM36,37Probable ubiquitin carboxyl-terminal hydrolase FAF-XUSP9X sp|Q93008-1|USP9X_HUMAN Isoform 2 of Probable ubiquitin carboxyl-terminal hydrolase FAF-X OS=Homo sapiens GN=USP9X;sp|Q93008|USP9X_HUMAN Probable ubiquitin carboxyl-terminal hydrolase FAF-X OS=Homo sapiens GN=USP9X PE=1 SV=336,09BRISC and BRCA1-A complex member 1 BABAM1 tr|M0R0I0|M0R0I0_HUMAN BRISC and BRCA1-A complex member 1 (Fragment) OS=Homo sapiens GN=BABAM1 PE=2 SV=1;tr|J3KQS6|J3KQS6_HUMAN BRISC and BRCA1-A complex member 1 OS=Homo sapiens GN=BABAM1 PE=2 SV=1;sp|Q9NWV8|BABA1_HUMAN BRISC and BRCA1-A complex member 1 35,41Cleavage and polyadenylation specificity factor subunit 6CPSF6 tr|F8WJN3|F8WJN3_HUMAN Cleavage and polyadenylation-specificity factor subunit 6 OS=Homo sapiens GN=CPSF6 PE=2 SV=1;sp|Q16630-3|CPSF6_HUMAN Isoform 3 of Cleavage and polyadenylation specificity factor subunit 6 OS=Homo sapiens GN=CPSF6;sp|Q16630|CPSF6_HUMA34,77DNA-directed RNA polymerases I, II, and III subunit RPABC3POLR2H tr|C9JLU1|C9JLU1_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC3 (Fragment) OS=Homo sapiens GN=POLR2H PE=2 SV=1;tr|C9JBJ6|C9JBJ6_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Homo sapiens GN=POLR2H PE=2 SV=1;sp|P5243433,88DNA-directed RNA polymerase II subunit GRINL1A;Putative GRINL1B complex locus protein 2POLR2M;GCOM1;GCOM2sp|P0CAP2|GRL1A_HUMAN DNA-directed RNA polymerase II subunit GRINL1A OS=Homo sapiens GN=POLR2M PE=1 SV=1;tr|H8Y6P7|H8Y6P7_HUMAN GRINL1A combined protein 15 OS=Homo sapiens GN=GCOM1 PE=2 SV=1;sp|P0CAP2-3|GRL1A_HUMAN Isoform 3 of DNA-directed RNA polymerase 33,7360S ribosomal protein L35 RPL35 sp|P42766|RL35_HUMAN 60S ribosomal protein L35 OS=Homo sapiens GN=RPL35 PE=1 SV=232,67BRISC complex subunit Abro1 FAM175B sp|Q15018|F175B_HUMAN BRISC complex subunit Abro1 OS=Homo sapiens GN=FAM175B PE=1 SV=231,31Protein UXT UXT sp|Q9UBK9|UXT_HUMAN Protein UXT OS=Homo sapiens GN=UXT PE=1 SV=131,17Protein PRRC2A PRRC2A sp|P48634|PRC2A_HUMAN Protein PRRC2A OS=Homo sapiens GN=PRRC2A PE=1 SV=3;sp|P48634-3|PRC2A_HUMAN Isoform 3 of Protein PRRC2A OS=Homo sapiens GN=PRRC2A;sp|P48634-2|PRC2A_HUMAN Isoform 2 of Protein PRRC2A OS=Homo sapiens GN=PRRC2A;sp|P48634-4|PRC2A_HUMAN Iso30,78DNA-directed RNA polymerase II subunit RPB11-a;DNA-directed RNA polymerase II subunit RPB11-b2;DNA-directed RNA polymerase II subunit RPB11-b1POLR2J;POLR2J1;POLR2J3;POLR2J2sp|P52435|RPB11_HUMAN DNA-directed RNA polymerase II subunit RPB11-a OS=Homo sapiens GN=POLR2J PE=1 SV=1;tr|Q9H1A6|Q9H1A6_HUMAN DNA-directed RNA polymerase II subunit RPB11-a OS=Homo sapiens GN=POLR2J1 PE=2 SV=1;tr|E2QRJ6|E2QRJ6_HUMAN DNA-directed RNA poly30,78DNA-directed RNA polymerases I, II, and III subunit RPABC1POLR2E sp|P19388|RPAB1_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Homo sapiens GN=POLR2E PE=1 SV=430,56Y-box-binding protein 3 YBX3 sp|P16989-2|YBOX3_HUMAN Isoform 2 of Y-box-binding protein 3 OS=Homo sapiens GN=YBX330,34NEDD4-like E3 ubiquitin-protein ligase WWP2WWP2 sp|O00308|WWP2_HUMAN NEDD4-like E3 ubiquitin-protein ligase WWP2 OS=Homo sapiens GN=WWP2 PE=1 SV=230,22ATP-dependent DNA helicase Q5 RECQL5 tr|Q6P4G0|Q6P4G0_HUMAN ATP-dependent DNA helicase Q5 OS=Homo sapiens GN=RECQL5 PE=2 SV=1;sp|O94762|RECQ5_HUMAN ATP-dependent DNA helicase Q5 OS=Homo sapiens GN=RECQL5 PE=1 SV=230,06Transcription elongation factor SPT5 SUPT5H sp|O00267-2|SPT5H_HUMAN Isoform 2 of Transcription elongation factor SPT5 OS=Homo sapiens GN=SUPT5H;sp|O00267|SPT5H_HUMAN Transcription elongation factor SPT5 OS=Homo sapiens GN=SUPT5H PE=1 SV=129,9160S ribosomal protein L8 RPL8 sp|P62917|RL8_HUMAN 60S ribosomal protein L8 OS=Homo sapiens GN=RPL8 PE=1 SV=2;tr|E9PKZ0|E9PKZ0_HUMAN 60S ribosomal protein L8 (Fragment) OS=Homo sapiens GN=RPL8 PE=2 SV=1;tr|G3V1A1|G3V1A1_HUMAN 60S ribosomal protein L8 OS=Homo sapiens GN=RPL8 PE=2 SV=1;tr29,79Replication factor C subunit 5 RFC5 sp|P40937-2|RFC5_HUMAN Isoform 2 of Replication factor C subunit 5 OS=Homo sapiens GN=RFC5;sp|P40937|RFC5_HUMAN Replication factor C subunit 5 OS=Homo sapiens GN=RFC5 PE=1 SV=1;tr|F5H304|F5H304_HUMAN Replication factor C subunit 5 (Fragment) OS=Homo sapien29,05General transcription factor IIF subunit 2 GTF2F2 sp|P13984|T2FB_HUMAN General transcription factor IIF subunit 2 OS=Homo sapiens GN=GTF2F2 PE=1 SV=228,69Eukaryotic translation initiation factor 3 subunit BEIF3B sp|P55884|EIF3B_HUMAN Eukaryotic translation initiation factor 3 subunit B OS=Homo sapiens GN=EIF3B PE=1 SV=3;sp|P55884-2|EIF3B_HUMAN Isoform 2 of Eukaryotic translation initiation factor 3 subunit B OS=Homo sapiens GN=EIF3B;tr|C9JZG1|C9JZG1_HUMAN Eukaryot28,42ATP-dependent RNA helicase A DHX9 sp|Q08211|DHX9_HUMAN ATP-dependent RNA helicase A OS=Homo sapiens GN=DHX9 PE=1 SV=428,37Transcription activator BRG1 SMARCA4 tr|Q9HBD4|Q9HBD4_HUMAN SMARCA4 isoform 2 OS=Homo sapiens GN=SMARCA4 PE=2 SV=1;sp|P51532-5|SMCA4_HUMAN Isoform 5 of Transcription activator BRG1 OS=Homo sapiens GN=SMARCA4;sp|P51532-2|SMCA4_HUMAN Isoform 2 of Transcription activator BRG1 OS=Homo sapiens GN=28,36Cleavage and polyadenylation specificity factor subunit 5NUDT21 sp|O43809|CPSF5_HUMAN Cleavage and polyadenylation specificity factor subunit 5 OS=Homo sapiens GN=NUDT21 PE=1 SV=1;tr|H3BND3|H3BND3_HUMAN Cleavage and polyadenylation-specificity factor subunit 5 (Fragment) OS=Homo sapiens GN=NUDT21 PE=2 SV=128,08DNA-directed RNA polymerase II subunit RPB1POLR2A sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 OS=Homo sapiens GN=POLR2A PE=1 SV=227,80DNA-directed RNA polymerases I, II, and III subunit RPABC5POLR2L sp|P62875|RPAB5_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Homo sapiens GN=POLR2L PE=1 SV=127,4360S acidic ribosomal protein P2 RPLP2 sp|P05387|RLA2_HUMAN 60S acidic ribosomal protein P2 OS=Homo sapiens GN=RPLP2 PE=1 SV=127,41Proliferation-associated protein 2G4 PA2G4 sp|Q9UQ80|PA2G4_HUMAN Proliferation-associated protein 2G4 OS=Homo sapiens GN=PA2G4 PE=1 SV=3;tr|F8VR77|F8VR77_HUMAN Proliferation-associated protein 2G4 OS=Homo sapiens GN=PA2G4 PE=2 SV=127,20Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2RPAP2 sp|Q8IXW5|RPAP2_HUMAN Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 OS=Homo sapiens GN=RPAP2 PE=1 SV=1;sp|Q8IXW5-2|RPAP2_HUMAN Isoform 2 of Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 OS=Homo sapiens GN=RPAP227,08Protein FAM168A FAM168A sp|Q92567-2|F168A_HUMAN Isoform 2 of Protein FAM168A OS=Homo sapiens GN=FAM168A;sp|Q92567|F168A_HUMAN Protein FAM168A OS=Homo sapiens GN=FAM168A PE=1 SV=226,88DNA-directed RNA polymerase II subunit RPB7POLR2G sp|P62487|RPB7_HUMAN DNA-directed RNA polymerase II subunit RPB7 OS=Homo sapiens GN=POLR2G PE=1 SV=126,7060S ribosomal protein L37;Ribosomal protein L37RPL37 sp|P61927|RL37_HUMAN 60S ribosomal protein L37 OS=Homo sapiens GN=RPL37 PE=1 SV=2;tr|D6RG19|D6RG19_HUMAN Ribosomal protein L37 OS=Homo sapiens GN=RPL37 PE=2 SV=126,6240S ribosomal protein S8 RPS8 tr|Q5JR95|Q5JR95_HUMAN 40S ribosomal protein S8 OS=Homo sapiens GN=RPS8 PE=2 SV=1;sp|P62241|RS8_HUMAN 40S ribosomal protein S8 OS=Homo sapiens GN=RPS8 PE=1 SV=226,5560S ribosomal protein L30 RPL30 sp|P62888|RL30_HUMAN 60S ribosomal protein L30 OS=Homo sapiens GN=RPL30 PE=1 SV=2;tr|E5RI99|E5RI99_HUMAN 60S ribosomal protein L30 (Fragment) OS=Homo sapiens GN=RPL30 PE=2 SV=126,3240S ribosomal protein S15a RPS15A sp|P62244|RS15A_HUMAN 40S ribosomal protein S15a OS=Homo sapiens GN=RPS15A PE=1 SV=2;tr|I3L3P7|I3L3P7_HUMAN 40S ribosomal protein S15a OS=Homo sapiens GN=RPS15A PE=2 SV=1;tr|I3L246|I3L246_HUMAN 40S ribosomal protein S15a OS=Homo sapiens GN=RPS15A PE=2 SV=126,1360S ribosomal protein L27 RPL27 sp|P61353|RL27_HUMAN 60S ribosomal protein L27 OS=Homo sapiens GN=RPL27 PE=1 SV=2;tr|K7ELC7|K7ELC7_HUMAN 60S ribosomal protein L27 (Fragment) OS=Homo sapiens GN=RPL27 PE=3 SV=1;tr|K7EQQ9|K7EQQ9_HUMAN 60S ribosomal protein L27 OS=Homo sapiens GN=RPL27 PE=2 25,89Transcription elongation factor SPT4 SUPT4H1 tr|D3DTZ5|D3DTZ5_HUMAN Suppressor of Ty 4 homolog 1 (S. cerevisiae), isoform CRA_b OS=Homo sapiens GN=SUPT4H1 PE=2 SV=1;tr|J3QSB9|J3QSB9_HUMAN Transcription elongation factor SPT4 OS=Homo sapiens GN=SUPT4H1 PE=2 SV=1;sp|P63272|SPT4H_HUMAN Transcription elo24,94RNA polymerase II-associated protein 3 RPAP3 sp|Q9H6T3|RPAP3_HUMAN RNA polymerase II-associated protein 3 OS=Homo sapiens GN=RPAP3 PE=1 SV=2;sp|Q9H6T3-2|RPAP3_HUMAN Isoform 2 of RNA polymerase II-associated protein 3 OS=Homo sapiens GN=RPAP3;sp|Q9H6T3-3|RPAP3_HUMAN Isoform 3 of RNA polymerase II-asso24,91WD repeat-containing protein 5 WDR5 sp|P61964|WDR5_HUMAN WD repeat-containing protein 5 OS=Homo sapiens GN=WDR5 PE=1 SV=124,90

Page 30: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

40S ribosomal protein S9 RPS9 sp|P46781|RS9_HUMAN 40S ribosomal protein S9 OS=Homo sapiens GN=RPS9 PE=1 SV=3;tr|B5MCT8|B5MCT8_HUMAN 40S ribosomal protein S9 OS=Homo sapiens GN=RPS9 PE=2 SV=1;tr|C9JM19|C9JM19_HUMAN 40S ribosomal protein S9 OS=Homo sapiens GN=RPS9 PE=2 SV=124,72Transducin beta-like protein 2 TBL2 tr|E9PF19|E9PF19_HUMAN Transducin beta-like protein 2 OS=Homo sapiens GN=TBL2 PE=2 SV=1;sp|Q9Y4P3|TBL2_HUMAN Transducin beta-like protein 2 OS=Homo sapiens GN=TBL2 PE=1 SV=1;tr|C9JVF0|C9JVF0_HUMAN Transducin beta-like protein 2 OS=Homo sapiens GN=TBL2 PE=224,57Histone H1.1 HIST1H1A sp|Q02539|H11_HUMAN Histone H1.1 OS=Homo sapiens GN=HIST1H1A PE=1 SV=324,4860S ribosomal protein L10 RPL10 tr|F8W7C6|F8W7C6_HUMAN 60S ribosomal protein L10 OS=Homo sapiens GN=RPL10 PE=2 SV=1;sp|P27635|RL10_HUMAN 60S ribosomal protein L10 OS=Homo sapiens GN=RPL10 PE=1 SV=4;tr|H7C123|H7C123_HUMAN 60S ribosomal protein L10 (Fragment) OS=Homo sapiens GN=RPL10 PE=2 24,45p53 and DNA damage-regulated protein 1 PDRG1 sp|Q9NUG6|PDRG1_HUMAN p53 and DNA damage-regulated protein 1 OS=Homo sapiens GN=PDRG1 PE=1 SV=224,4160S ribosomal protein L32 RPL32 tr|F8W727|F8W727_HUMAN 60S ribosomal protein L32 OS=Homo sapiens GN=RPL32 PE=2 SV=1;sp|P62910|RL32_HUMAN 60S ribosomal protein L32 OS=Homo sapiens GN=RPL32 PE=1 SV=2;tr|D3YTB1|D3YTB1_HUMAN 60S ribosomal protein L32 (Fragment) OS=Homo sapiens GN=RPL32 PE=2 24,3260S ribosomal protein L22 RPL22 tr|K7EP65|K7EP65_HUMAN 60S ribosomal protein L22 (Fragment) OS=Homo sapiens GN=RPL22 PE=2 SV=1;tr|K7EKS7|K7EKS7_HUMAN 60S ribosomal protein L22 OS=Homo sapiens GN=RPL22 PE=2 SV=1;tr|K7ELC4|K7ELC4_HUMAN 60S ribosomal protein L22 (Fragment) OS=Homo sapiens G24,2840S ribosomal protein S16 RPS16 sp|P62249|RS16_HUMAN 40S ribosomal protein S16 OS=Homo sapiens GN=RPS16 PE=1 SV=2;tr|M0R210|M0R210_HUMAN 40S ribosomal protein S16 OS=Homo sapiens GN=RPS16 PE=2 SV=1;tr|M0R3H0|M0R3H0_HUMAN 40S ribosomal protein S16 OS=Homo sapiens GN=RPS16 PE=2 SV=1;tr|M0R24,27ATP-dependent RNA helicase DDX1 DDX1 sp|Q92499|DDX1_HUMAN ATP-dependent RNA helicase DDX1 OS=Homo sapiens GN=DDX1 PE=1 SV=224,1840S ribosomal protein S6 RPS6 sp|P62753|RS6_HUMAN 40S ribosomal protein S6 OS=Homo sapiens GN=RPS6 PE=1 SV=1;tr|A2A3R5|A2A3R5_HUMAN 40S ribosomal protein S6 OS=Homo sapiens GN=RPS6 PE=2 SV=124,1260S ribosomal protein L22-like 1 RPL22L1 tr|C9JYQ9|C9JYQ9_HUMAN 60S ribosomal protein L22-like 1 OS=Homo sapiens GN=RPL22L1 PE=2 SV=1;tr|H0Y8C2|H0Y8C2_HUMAN 60S ribosomal protein L22-like 1 (Fragment) OS=Homo sapiens GN=RPL22L1 PE=2 SV=1;sp|Q6P5R6|RL22L_HUMAN 60S ribosomal protein L22-like 1 OS=H24,1240S ribosomal protein S3a RPS3A sp|P61247|RS3A_HUMAN 40S ribosomal protein S3a OS=Homo sapiens GN=RPS3A PE=1 SV=2;tr|F5H4F9|F5H4F9_HUMAN 40S ribosomal protein S3a OS=Homo sapiens GN=RPS3A PE=2 SV=1;tr|E9PFI5|E9PFI5_HUMAN 40S ribosomal protein S3a OS=Homo sapiens GN=RPS3A PE=2 SV=1;tr|D6R23,9040S ribosomal protein SA RPSA;RPSAP58 tr|C9J9K3|C9J9K3_HUMAN 40S ribosomal protein SA (Fragment) OS=Homo sapiens GN=RPSA PE=2 SV=1;sp|P08865|RSSA_HUMAN 40S ribosomal protein SA OS=Homo sapiens GN=RPSA PE=1 SV=4;tr|A6NE09|A6NE09_HUMAN 40S ribosomal protein SA OS=Homo sapiens GN=RPSAP58 PE=2 SV=23,8540S ribosomal protein S29 RPS29 sp|P62273|RS29_HUMAN 40S ribosomal protein S29 OS=Homo sapiens GN=RPS29 PE=1 SV=2;sp|P62273-2|RS29_HUMAN Isoform 2 of 40S ribosomal protein S29 OS=Homo sapiens GN=RPS2923,7760S ribosomal protein L7 RPL7 sp|P18124|RL7_HUMAN 60S ribosomal protein L7 OS=Homo sapiens GN=RPL7 PE=1 SV=1;tr|A8MUD9|A8MUD9_HUMAN 60S ribosomal protein L7 OS=Homo sapiens GN=RPL7 PE=2 SV=123,7540S ribosomal protein S23 RPS23 sp|P62266|RS23_HUMAN 40S ribosomal protein S23 OS=Homo sapiens GN=RPS23 PE=1 SV=3;tr|D6RD47|D6RD47_HUMAN 40S ribosomal protein S23 OS=Homo sapiens GN=RPS23 PE=2 SV=123,3860S ribosomal protein L13 RPL13 sp|P26373|RL13_HUMAN 60S ribosomal protein L13 OS=Homo sapiens GN=RPL13 PE=1 SV=4;sp|P26373-2|RL13_HUMAN Isoform 2 of 60S ribosomal protein L13 OS=Homo sapiens GN=RPL1323,31Lys-63-specific deubiquitinase BRCC36 BRCC3 sp|P46736-2|BRCC3_HUMAN Isoform 1 of Lys-63-specific deubiquitinase BRCC36 OS=Homo sapiens GN=BRCC3;sp|P46736-3|BRCC3_HUMAN Isoform 3 of Lys-63-specific deubiquitinase BRCC36 OS=Homo sapiens GN=BRCC3;sp|P46736|BRCC3_HUMAN Lys-63-specific deubiquitinase BRC23,2960S ribosomal protein L6 RPL6 sp|Q02878|RL6_HUMAN 60S ribosomal protein L6 OS=Homo sapiens GN=RPL6 PE=1 SV=323,2360S ribosomal protein L3 RPL3 sp|P39023|RL3_HUMAN 60S ribosomal protein L3 OS=Homo sapiens GN=RPL3 PE=1 SV=2;tr|H7C3M2|H7C3M2_HUMAN 60S ribosomal protein L3 (Fragment) OS=Homo sapiens GN=RPL3 PE=4 SV=1;tr|H7C422|H7C422_HUMAN 60S ribosomal protein L3 (Fragment) OS=Homo sapiens GN=RPL3 P23,1740S ribosomal protein S14 RPS14 sp|P62263|RS14_HUMAN 40S ribosomal protein S14 OS=Homo sapiens GN=RPS14 PE=1 SV=3;tr|H0YB22|H0YB22_HUMAN 40S ribosomal protein S14 (Fragment) OS=Homo sapiens GN=RPS14 PE=4 SV=1;tr|E5RH77|E5RH77_HUMAN 40S ribosomal protein S14 OS=Homo sapiens GN=RPS14 PE=2 23,1440S ribosomal protein S24 RPS24 tr|E7ETK0|E7ETK0_HUMAN 40S ribosomal protein S24 OS=Homo sapiens GN=RPS24 PE=2 SV=1;sp|P62847-2|RS24_HUMAN Isoform 2 of 40S ribosomal protein S24 OS=Homo sapiens GN=RPS24;sp|P62847-3|RS24_HUMAN Isoform 3 of 40S ribosomal protein S24 OS=Homo sapiens GN=RPS223,10Ribosomal protein L19;60S ribosomal protein L19RPL19 tr|J3QR09|J3QR09_HUMAN Ribosomal protein L19 OS=Homo sapiens GN=RPL19 PE=2 SV=1;tr|J3KTE4|J3KTE4_HUMAN Ribosomal protein L19 OS=Homo sapiens GN=RPL19 PE=2 SV=1;sp|P84098|RL19_HUMAN 60S ribosomal protein L19 OS=Homo sapiens GN=RPL19 PE=1 SV=123,10Ras GTPase-activating protein-binding protein 1G3BP1 sp|Q13283|G3BP1_HUMAN Ras GTPase-activating protein-binding protein 1 OS=Homo sapiens GN=G3BP1 PE=1 SV=1;tr|F5H4D6|F5H4D6_HUMAN Ras GTPase-activating protein-binding protein 1 OS=Homo sapiens GN=G3BP1 PE=2 SV=123,07Polyadenylate-binding protein 1;Polyadenylate-binding protein;Polyadenylate-binding protein 3PABPC1;PABPC3 sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=PABPC1 PE=1 SV=2;tr|E7EQV3|E7EQV3_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=PABPC1 PE=2 SV=1;tr|E7ERJ7|E7ERJ7_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=P23,06Putative 60S ribosomal protein L39-like 5;60S ribosomal protein L39RPL39P5;RPL39 sp|Q59GN2|R39L5_HUMAN Putative 60S ribosomal protein L39-like 5 OS=Homo sapiens GN=RPL39P5 PE=5 SV=2;sp|P62891|RL39_HUMAN 60S ribosomal protein L39 OS=Homo sapiens GN=RPL39 PE=1 SV=223,06Ras GTPase-activating protein-binding protein 2G3BP2 sp|Q9UN86-2|G3BP2_HUMAN Isoform B of Ras GTPase-activating protein-binding protein 2 OS=Homo sapiens GN=G3BP2;sp|Q9UN86|G3BP2_HUMAN Ras GTPase-activating protein-binding protein 2 OS=Homo sapiens GN=G3BP2 PE=1 SV=2;tr|D6RAC7|D6RAC7_HUMAN Ras GTPase-activat22,9740S ribosomal protein S15 RPS15 tr|K7EM56|K7EM56_HUMAN 40S ribosomal protein S15 OS=Homo sapiens GN=RPS15 PE=3 SV=2;tr|K7EQJ5|K7EQJ5_HUMAN 40S ribosomal protein S15 OS=Homo sapiens GN=RPS15 PE=2 SV=2;tr|K7ELC2|K7ELC2_HUMAN 40S ribosomal protein S15 OS=Homo sapiens GN=RPS15 PE=2 SV=1;sp|P22,89Interleukin enhancer-binding factor 2 ILF2 sp|Q12905|ILF2_HUMAN Interleukin enhancer-binding factor 2 OS=Homo sapiens GN=ILF2 PE=1 SV=222,8760S ribosomal protein L27a RPL27A tr|E9PLL6|E9PLL6_HUMAN 60S ribosomal protein L27a OS=Homo sapiens GN=RPL27A PE=2 SV=1;sp|P46776|RL27A_HUMAN 60S ribosomal protein L27a OS=Homo sapiens GN=RPL27A PE=1 SV=2;tr|E9PJD9|E9PJD9_HUMAN 60S ribosomal protein L27a OS=Homo sapiens GN=RPL27A PE=2 SV=122,8140S ribosomal protein S12 RPS12 sp|P25398|RS12_HUMAN 40S ribosomal protein S12 OS=Homo sapiens GN=RPS12 PE=1 SV=322,6960S ribosomal protein L35a RPL35A sp|P18077|RL35A_HUMAN 60S ribosomal protein L35a OS=Homo sapiens GN=RPL35A PE=1 SV=2;tr|C9K025|C9K025_HUMAN 60S ribosomal protein L35a (Fragment) OS=Homo sapiens GN=RPL35A PE=2 SV=1;tr|F8WBS5|F8WBS5_HUMAN 60S ribosomal protein L35a OS=Homo sapiens GN=RPL3522,5940S ribosomal protein S13 RPS13 sp|P62277|RS13_HUMAN 40S ribosomal protein S13 OS=Homo sapiens GN=RPS13 PE=1 SV=2;tr|J3KMX5|J3KMX5_HUMAN 40S ribosomal protein S13 OS=Homo sapiens GN=RPS13 PE=2 SV=122,5440S ribosomal protein S11 RPS11 tr|M0QZC5|M0QZC5_HUMAN 40S ribosomal protein S11 OS=Homo sapiens GN=RPS11 PE=2 SV=1;sp|P62280|RS11_HUMAN 40S ribosomal protein S11 OS=Homo sapiens GN=RPS11 PE=1 SV=3;tr|M0R1H6|M0R1H6_HUMAN 40S ribosomal protein S11 OS=Homo sapiens GN=RPS11 PE=2 SV=122,5040S ribosomal protein S28 RPS28 sp|P62857|RS28_HUMAN 40S ribosomal protein S28 OS=Homo sapiens GN=RPS28 PE=1 SV=122,3360S ribosomal protein L26 RPL26 sp|P61254|RL26_HUMAN 60S ribosomal protein L26 OS=Homo sapiens GN=RPL26 PE=1 SV=1;tr|J3QRI7|J3QRI7_HUMAN 60S ribosomal protein L26 (Fragment) OS=Homo sapiens GN=RPL26 PE=2 SV=1;tr|J3QQQ9|J3QQQ9_HUMAN KRAB-A domain-containing protein 2 OS=Homo sapiens GN=KR22,2060S ribosomal protein L14 RPL14 sp|P50914|RL14_HUMAN 60S ribosomal protein L14 OS=Homo sapiens GN=RPL14 PE=1 SV=4;tr|E7EPB3|E7EPB3_HUMAN 60S ribosomal protein L14 OS=Homo sapiens GN=RPL14 PE=2 SV=122,1440S ribosomal protein S25 RPS25 sp|P62851|RS25_HUMAN 40S ribosomal protein S25 OS=Homo sapiens GN=RPS25 PE=1 SV=122,1360S ribosomal protein L31 RPL31 sp|P62899|RL31_HUMAN 60S ribosomal protein L31 OS=Homo sapiens GN=RPL31 PE=1 SV=1;tr|H7C2W9|H7C2W9_HUMAN 60S ribosomal protein L31 (Fragment) OS=Homo sapiens GN=RPL31 PE=4 SV=1;tr|C9JU56|C9JU56_HUMAN 60S ribosomal protein L31 (Fragment) OS=Homo sapiens GN=21,8260S ribosomal protein L4 RPL4 sp|P36578|RL4_HUMAN 60S ribosomal protein L4 OS=Homo sapiens GN=RPL4 PE=1 SV=5;tr|H3BM89|H3BM89_HUMAN 60S ribosomal protein L4 OS=Homo sapiens GN=RPL4 PE=2 SV=121,67Nucleophosmin NPM1 sp|P06748-3|NPM_HUMAN Isoform 3 of Nucleophosmin OS=Homo sapiens GN=NPM1;sp|P06748|NPM_HUMAN Nucleophosmin OS=Homo sapiens GN=NPM1 PE=1 SV=2;sp|P06748-2|NPM_HUMAN Isoform 2 of Nucleophosmin OS=Homo sapiens GN=NPM121,46Angiomotin AMOT sp|Q4VCS5|AMOT_HUMAN Angiomotin OS=Homo sapiens GN=AMOT PE=1 SV=1;tr|E7ERM3|E7ERM3_HUMAN Angiomotin OS=Homo sapiens GN=AMOT PE=2 SV=1;tr|A6NP16|A6NP16_HUMAN Angiomotin OS=Homo sapiens GN=AMOT PE=2 SV=1;sp|Q4VCS5-2|AMOT_HUMAN Isoform 2 of Angiomotin OS=Homo21,42Serine/arginine-rich splicing factor 7 SRSF7 tr|C9JAB2|C9JAB2_HUMAN Serine/arginine-rich-splicing factor 7 OS=Homo sapiens GN=SRSF7 PE=2 SV=1;sp|Q16629-3|SRSF7_HUMAN Isoform 3 of Serine/arginine-rich splicing factor 7 OS=Homo sapiens GN=SRSF7;sp|Q16629-2|SRSF7_HUMAN Isoform 2 of Serine/arginine-rich 21,38Splicing factor, proline- and glutamine-rich SFPQ sp|P23246|SFPQ_HUMAN Splicing factor, proline- and glutamine-rich OS=Homo sapiens GN=SFPQ PE=1 SV=2;sp|P23246-2|SFPQ_HUMAN Isoform Short of Splicing factor, proline- and glutamine-rich OS=Homo sapiens GN=SFPQ;tr|H0Y9K7|H0Y9K7_HUMAN Splicing factor, proline21,33USP6 N-terminal-like protein USP6NL sp|Q92738|US6NL_HUMAN USP6 N-terminal-like protein OS=Homo sapiens GN=USP6NL PE=1 SV=3;sp|Q92738-2|US6NL_HUMAN Isoform 2 of USP6 N-terminal-like protein OS=Homo sapiens GN=USP6NL21,2960S ribosomal protein L12 RPL12 sp|P30050|RL12_HUMAN 60S ribosomal protein L12 OS=Homo sapiens GN=RPL12 PE=1 SV=121,1860S acidic ribosomal protein P1 RPLP1 sp|P05386|RLA1_HUMAN 60S acidic ribosomal protein P1 OS=Homo sapiens GN=RPLP1 PE=1 SV=121,1740S ribosomal protein S18 RPS18 sp|P62269|RS18_HUMAN 40S ribosomal protein S18 OS=Homo sapiens GN=RPS18 PE=1 SV=321,15Kinesin-like protein KIF2A KIF2A sp|O00139-2|KIF2A_HUMAN Isoform 2 of Kinesin-like protein KIF2A OS=Homo sapiens GN=KIF2A;sp|O00139-1|KIF2A_HUMAN Isoform 1 of Kinesin-like protein KIF2A OS=Homo sapiens GN=KIF2A;sp|O00139-5|KIF2A_HUMAN Isoform 5 of Kinesin-like protein KIF2A OS=Homo sapien21,0960S ribosomal protein L23 RPL23 sp|P62829|RL23_HUMAN 60S ribosomal protein L23 OS=Homo sapiens GN=RPL23 PE=1 SV=1;tr|J3KT29|J3KT29_HUMAN 60S ribosomal protein L23 OS=Homo sapiens GN=RPL23 PE=2 SV=1;tr|C9JD32|C9JD32_HUMAN 60S ribosomal protein L23 (Fragment) OS=Homo sapiens GN=RPL23 PE=2 21,0440S ribosomal protein S7 RPS7 sp|P62081|RS7_HUMAN 40S ribosomal protein S7 OS=Homo sapiens GN=RPS7 PE=1 SV=1;tr|B5MCP9|B5MCP9_HUMAN 40S ribosomal protein S7 OS=Homo sapiens GN=RPS7 PE=2 SV=121,0360S ribosomal protein L13a;Putative 60S ribosomal protein L13a protein RPL13AP3RPL13A;RPL13AP3 sp|P40429|RL13A_HUMAN 60S ribosomal protein L13a OS=Homo sapiens GN=RPL13A PE=1 SV=2;tr|M0QYS1|M0QYS1_HUMAN 60S ribosomal protein L13a (Fragment) OS=Homo sapiens GN=RPL13A PE=2 SV=2;sp|Q6NVV1|R13AX_HUMAN Putative 60S ribosomal protein L13a-like MGC87657 OS20,9960S ribosomal protein L5 RPL5 sp|P46777|RL5_HUMAN 60S ribosomal protein L5 OS=Homo sapiens GN=RPL5 PE=1 SV=320,9640S ribosomal protein S19 RPS19 sp|P39019|RS19_HUMAN 40S ribosomal protein S19 OS=Homo sapiens GN=RPS19 PE=1 SV=220,9460S ribosomal protein L18a RPL18A tr|M0R3D6|M0R3D6_HUMAN 60S ribosomal protein L18a (Fragment) OS=Homo sapiens GN=RPL18A PE=2 SV=1;tr|M0R1A7|M0R1A7_HUMAN 60S ribosomal protein L18a OS=Homo sapiens GN=RPL18A PE=2 SV=1;tr|M0R117|M0R117_HUMAN 60S ribosomal protein L18a OS=Homo sapiens GN=RPL120,9460S ribosomal protein L15;Ribosomal protein L15RPL15 sp|P61313|RL15_HUMAN 60S ribosomal protein L15 OS=Homo sapiens GN=RPL15 PE=1 SV=2;tr|E7EQV9|E7EQV9_HUMAN Ribosomal protein L15 (Fragment) OS=Homo sapiens GN=RPL15 PE=2 SV=1;tr|E7ENU7|E7ENU7_HUMAN Ribosomal protein L15 (Fragment) OS=Homo sapiens GN=RPL15 PE20,82

Page 31: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-likeRPLP0;RPLP0P6 sp|P05388|RLA0_HUMAN 60S acidic ribosomal protein P0 OS=Homo sapiens GN=RPLP0 PE=1 SV=1;tr|F8VWS0|F8VWS0_HUMAN 60S acidic ribosomal protein P0 OS=Homo sapiens GN=RPLP0 PE=2 SV=1;tr|Q3B7A4|Q3B7A4_HUMAN 60S acidic ribosomal protein P0 OS=Homo sapiens GN=RPLP20,82RuvB-like 1 RUVBL1 sp|Q9Y265|RUVB1_HUMAN RuvB-like 1 OS=Homo sapiens GN=RUVBL1 PE=1 SV=1;sp|Q9Y265-2|RUVB1_HUMAN Isoform 2 of RuvB-like 1 OS=Homo sapiens GN=RUVBL1;tr|E7ETR0|E7ETR0_HUMAN RuvB-like 1 OS=Homo sapiens GN=RUVBL1 PE=2 SV=120,7940S ribosomal protein S20 RPS20 sp|P60866|RS20_HUMAN 40S ribosomal protein S20 OS=Homo sapiens GN=RPS20 PE=1 SV=1;sp|P60866-2|RS20_HUMAN Isoform 2 of 40S ribosomal protein S20 OS=Homo sapiens GN=RPS20;tr|E5RIP1|E5RIP1_HUMAN 40S ribosomal protein S20 OS=Homo sapiens GN=RPS20 PE=2 SV=1;tr|20,7660S ribosomal protein L7a RPL7A sp|P62424|RL7A_HUMAN 60S ribosomal protein L7a OS=Homo sapiens GN=RPL7A PE=1 SV=2;tr|Q5T8U3|Q5T8U3_HUMAN 60S ribosomal protein L7a (Fragment) OS=Homo sapiens GN=RPL7A PE=2 SV=120,7160S ribosomal protein L37a;Putative 60S ribosomal protein L37a-like proteinRPL37A;RPL37AP8 tr|C9J4Z3|C9J4Z3_HUMAN 60S ribosomal protein L37a OS=Homo sapiens GN=RPL37A PE=2 SV=1;sp|P61513|RL37A_HUMAN 60S ribosomal protein L37a OS=Homo sapiens GN=RPL37A PE=1 SV=2;sp|A6NKH3|RL37L_HUMAN Putative 60S ribosomal protein L37a-like OS=Homo sapiens GN=RPL20,64Fragile X mental retardation syndrome-related protein 1FXR1 sp|P51114|FXR1_HUMAN Fragile X mental retardation syndrome-related protein 1 OS=Homo sapiens GN=FXR1 PE=1 SV=3;tr|B4DXZ6|B4DXZ6_HUMAN Fragile X mental retardation syndrome-related protein 1 OS=Homo sapiens GN=FXR1 PE=2 SV=1;sp|P51114-2|FXR1_HUMAN Isoform 220,64Heterogeneous nuclear ribonucleoprotein M HNRNPM sp|P52272-2|HNRPM_HUMAN Isoform 2 of Heterogeneous nuclear ribonucleoprotein M OS=Homo sapiens GN=HNRNPM;sp|P52272|HNRPM_HUMAN Heterogeneous nuclear ribonucleoprotein M OS=Homo sapiens GN=HNRNPM PE=1 SV=320,58RuvB-like 2 RUVBL2 sp|Q9Y230|RUVB2_HUMAN RuvB-like 2 OS=Homo sapiens GN=RUVBL2 PE=1 SV=3;tr|B3KQ59|B3KQ59_HUMAN RuvB-like 2 OS=Homo sapiens GN=RUVBL2 PE=2 SV=1;tr|M0R0Y3|M0R0Y3_HUMAN RuvB-like 2 OS=Homo sapiens GN=RUVBL2 PE=2 SV=120,5640S ribosomal protein S27 RPS27 tr|Q5T4L4|Q5T4L4_HUMAN 40S ribosomal protein S27 OS=Homo sapiens GN=RPS27 PE=2 SV=1;sp|P42677|RS27_HUMAN 40S ribosomal protein S27 OS=Homo sapiens GN=RPS27 PE=1 SV=320,50Interleukin enhancer-binding factor 3 ILF3 sp|Q12906|ILF3_HUMAN Interleukin enhancer-binding factor 3 OS=Homo sapiens GN=ILF3 PE=1 SV=3;sp|Q12906-7|ILF3_HUMAN Isoform 7 of Interleukin enhancer-binding factor 3 OS=Homo sapiens GN=ILF3;sp|Q12906-5|ILF3_HUMAN Isoform 5 of Interleukin enhancer-binding 20,47Eukaryotic translation initiation factor 3 subunit AEIF3A sp|Q14152|EIF3A_HUMAN Eukaryotic translation initiation factor 3 subunit A OS=Homo sapiens GN=EIF3A PE=1 SV=1;tr|F5H335|F5H335_HUMAN Eukaryotic translation initiation factor 3 subunit A OS=Homo sapiens GN=EIF3A PE=2 SV=120,4160S ribosomal protein L36 RPL36 sp|Q9Y3U8|RL36_HUMAN 60S ribosomal protein L36 OS=Homo sapiens GN=RPL36 PE=1 SV=320,4040S ribosomal protein S10;Putative 40S ribosomal protein S10-likeRPS10;RPS10-NUDT3;RPS10P5sp|P46783|RS10_HUMAN 40S ribosomal protein S10 OS=Homo sapiens GN=RPS10 PE=1 SV=1;tr|F6U211|F6U211_HUMAN 40S ribosomal protein S10 OS=Homo sapiens GN=RPS10 PE=2 SV=1;tr|S4R435|S4R435_HUMAN Protein RPS10-NUDT3 (Fragment) OS=Homo sapiens GN=RPS10-NUDT3 PE=3 20,3060S ribosomal protein L18 RPL18 tr|G3V203|G3V203_HUMAN 60S ribosomal protein L18 OS=Homo sapiens GN=RPL18 PE=2 SV=1;tr|J3QQ67|J3QQ67_HUMAN 60S ribosomal protein L18 (Fragment) OS=Homo sapiens GN=RPL18 PE=3 SV=1;sp|Q07020|RL18_HUMAN 60S ribosomal protein L18 OS=Homo sapiens GN=RPL18 PE=1 20,28Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like proteinEIF3C;EIF3CL tr|H3BRV0|H3BRV0_HUMAN Eukaryotic translation initiation factor 3 subunit C OS=Homo sapiens GN=EIF3C PE=2 SV=1;sp|Q99613|EIF3C_HUMAN Eukaryotic translation initiation factor 3 subunit C OS=Homo sapiens GN=EIF3C PE=1 SV=1;sp|B5ME19|EIFCL_HUMAN Eukaryotic tr20,23Prolyl 3-hydroxylase 3 LEPREL2 tr|G8JLI6|G8JLI6_HUMAN Prolyl 3-hydroxylase 3 OS=Homo sapiens GN=LEPREL2 PE=2 SV=1;sp|Q8IVL6|P3H3_HUMAN Prolyl 3-hydroxylase 3 OS=Homo sapiens GN=LEPREL2 PE=1 SV=1;sp|Q8IVL6-2|P3H3_HUMAN Isoform 2 of Prolyl 3-hydroxylase 3 OS=Homo sapiens GN=LEPREL220,22Serine/arginine-rich splicing factor 1 SRSF1 tr|J3KTL2|J3KTL2_HUMAN Serine/arginine-rich-splicing factor 1 OS=Homo sapiens GN=SRSF1 PE=2 SV=1;sp|Q07955|SRSF1_HUMAN Serine/arginine-rich splicing factor 1 OS=Homo sapiens GN=SRSF1 PE=1 SV=2;sp|Q07955-3|SRSF1_HUMAN Isoform ASF-3 of Serine/arginine-rich s20,2040S ribosomal protein S2 RPS2 sp|P15880|RS2_HUMAN 40S ribosomal protein S2 OS=Homo sapiens GN=RPS2 PE=1 SV=2;tr|H0YEN5|H0YEN5_HUMAN 40S ribosomal protein S2 (Fragment) OS=Homo sapiens GN=RPS2 PE=2 SV=1;tr|E9PQD7|E9PQD7_HUMAN 40S ribosomal protein S2 OS=Homo sapiens GN=RPS2 PE=2 SV=1;tr20,2060S ribosomal protein L34 RPL34 sp|P49207|RL34_HUMAN 60S ribosomal protein L34 OS=Homo sapiens GN=RPL34 PE=1 SV=320,0360S ribosomal protein L21 RPL21 sp|P46778|RL21_HUMAN 60S ribosomal protein L21 OS=Homo sapiens GN=RPL21 PE=1 SV=2;tr|G3V1B3|G3V1B3_HUMAN 60S ribosomal protein L21 OS=Homo sapiens GN=RPL21 PE=4 SV=1;tr|M0R181|M0R181_HUMAN 60S ribosomal protein L21 (Fragment) OS=Homo sapiens GN=RPL21 PE=4 20,01Probable ATP-dependent RNA helicase DDX47DDX47 sp|Q9H0S4|DDX47_HUMAN Probable ATP-dependent RNA helicase DDX47 OS=Homo sapiens GN=DDX47 PE=1 SV=1;sp|Q9H0S4-2|DDX47_HUMAN Isoform 2 of Probable ATP-dependent RNA helicase DDX47 OS=Homo sapiens GN=DDX4719,9340S ribosomal protein S5;40S ribosomal protein S5, N-terminally processedRPS5 tr|M0R0F0|M0R0F0_HUMAN 40S ribosomal protein S5 (Fragment) OS=Homo sapiens GN=RPS5 PE=2 SV=1;tr|M0R0R2|M0R0R2_HUMAN 40S ribosomal protein S5 OS=Homo sapiens GN=RPS5 PE=2 SV=1;sp|P46782|RS5_HUMAN 40S ribosomal protein S5 OS=Homo sapiens GN=RPS5 PE=1 SV=419,92Tyrosine-protein phosphatase non-receptor type 14PTPN14 sp|Q15678|PTN14_HUMAN Tyrosine-protein phosphatase non-receptor type 14 OS=Homo sapiens GN=PTPN14 PE=1 SV=219,8460S ribosomal protein L11 RPL11 sp|P62913-2|RL11_HUMAN Isoform 2 of 60S ribosomal protein L11 OS=Homo sapiens GN=RPL11;sp|P62913|RL11_HUMAN 60S ribosomal protein L11 OS=Homo sapiens GN=RPL11 PE=1 SV=2;tr|Q5VVC8|Q5VVC8_HUMAN 60S ribosomal protein L11 (Fragment) OS=Homo sapiens GN=RPL11 PE19,7660S ribosomal protein L23a RPL23A sp|P62750|RL23A_HUMAN 60S ribosomal protein L23a OS=Homo sapiens GN=RPL23A PE=1 SV=1;tr|H7BY10|H7BY10_HUMAN 60S ribosomal protein L23a (Fragment) OS=Homo sapiens GN=RPL23A PE=3 SV=1;tr|K7EJV9|K7EJV9_HUMAN 60S ribosomal protein L23a (Fragment) OS=Homo sapie19,75Serine/arginine-rich splicing factor 6 SRSF6 sp|Q13247-3|SRSF6_HUMAN Isoform SRP55-3 of Serine/arginine-rich splicing factor 6 OS=Homo sapiens GN=SRSF6;sp|Q13247|SRSF6_HUMAN Serine/arginine-rich splicing factor 6 OS=Homo sapiens GN=SRSF6 PE=1 SV=2;sp|Q13247-2|SRSF6_HUMAN Isoform SRP55-2 of Serine/arg19,7460S ribosomal protein L9 RPL9 tr|D6RAN4|D6RAN4_HUMAN 60S ribosomal protein L9 (Fragment) OS=Homo sapiens GN=RPL9 PE=2 SV=1;sp|P32969|RL9_HUMAN 60S ribosomal protein L9 OS=Homo sapiens GN=RPL9 PE=1 SV=1;tr|H0Y9V9|H0Y9V9_HUMAN 60S ribosomal protein L9 (Fragment) OS=Homo sapiens GN=RPL9 P19,66Eukaryotic translation initiation factor 3 subunit HEIF3H tr|B3KS98|B3KS98_HUMAN Eukaryotic translation initiation factor 3 subunit H OS=Homo sapiens GN=EIF3S3 PE=2 SV=1;sp|O15372|EIF3H_HUMAN Eukaryotic translation initiation factor 3 subunit H OS=Homo sapiens GN=EIF3H PE=1 SV=1;tr|E5RJT0|E5RJT0_HUMAN Eukaryotic 19,65Protein PRRC2C PRRC2C tr|E7EPN9|E7EPN9_HUMAN Protein PRRC2C OS=Homo sapiens GN=PRRC2C PE=2 SV=1;sp|Q9Y520-4|PRC2C_HUMAN Isoform 4 of Protein PRRC2C OS=Homo sapiens GN=PRRC2C;sp|Q9Y520-5|PRC2C_HUMAN Isoform 5 of Protein PRRC2C OS=Homo sapiens GN=PRRC2C;sp|Q9Y520|PRC2C_HUMAN Prot19,6440S ribosomal protein S3 RPS3 sp|P23396|RS3_HUMAN 40S ribosomal protein S3 OS=Homo sapiens GN=RPS3 PE=1 SV=2;tr|E9PL09|E9PL09_HUMAN 40S ribosomal protein S3 OS=Homo sapiens GN=RPS3 PE=2 SV=1;sp|P23396-2|RS3_HUMAN Isoform 2 of 40S ribosomal protein S3 OS=Homo sapiens GN=RPS3;tr|E9PPU1|E19,6360S ribosomal protein L36a RPL36A;RPL36A-HNRNPH2tr|J3KQN4|J3KQN4_HUMAN 60S ribosomal protein L36a OS=Homo sapiens GN=RPL36A PE=2 SV=1;sp|P83881|RL36A_HUMAN 60S ribosomal protein L36a OS=Homo sapiens GN=RPL36A PE=1 SV=2;tr|H7BZ11|H7BZ11_HUMAN Protein RPL36A-HNRNPH2 (Fragment) OS=Homo sapiens GN=RPL36A-HN19,58Eukaryotic translation initiation factor 3 subunit FEIF3F tr|B3KSH1|B3KSH1_HUMAN Eukaryotic translation initiation factor 3 subunit F OS=Homo sapiens GN=EIF3F PE=2 SV=1;sp|O00303|EIF3F_HUMAN Eukaryotic translation initiation factor 3 subunit F OS=Homo sapiens GN=EIF3F PE=1 SV=1;tr|B4DEW9|B4DEW9_HUMAN Eukaryotic t19,5760S ribosomal protein L17 RPL17 tr|J3QQT2|J3QQT2_HUMAN 60S ribosomal protein L17 (Fragment) OS=Homo sapiens GN=RPL17 PE=2 SV=1;tr|J3KRX5|J3KRX5_HUMAN 60S ribosomal protein L17 (Fragment) OS=Homo sapiens GN=RPL17 PE=2 SV=1;sp|P18621|RL17_HUMAN 60S ribosomal protein L17 OS=Homo sapiens GN=19,53Cancer/testis antigen family 45 member A3;Cancer/testis antigen family 45 member A4;Cancer/testis antigen family 45 member A10;Cancer/testis antigen family 45 member A1;Cancer/testis antigen family 45 member A2CT45A3;CT45A4;CT45A10;CT45A1;CT45A2sp|Q8NHU0|CT453_HUMAN Cancer/testis antigen family 45 member A3 OS=Homo sapiens GN=CT45A3 PE=2 SV=1;sp|Q8N7B7|CT454_HUMAN Cancer/testis antigen family 45 member A4/A6 OS=Homo sapiens GN=CT45A4 PE=2 SV=1;sp|Q6NSH3|CT455_HUMAN Cancer/testis antigen family 4519,52Plasminogen activator inhibitor 1 RNA-binding proteinSERBP1 sp|Q8NC51-3|PAIRB_HUMAN Isoform 3 of Plasminogen activator inhibitor 1 RNA-binding protein OS=Homo sapiens GN=SERBP1;sp|Q8NC51|PAIRB_HUMAN Plasminogen activator inhibitor 1 RNA-binding protein OS=Homo sapiens GN=SERBP1 PE=1 SV=2;sp|Q8NC51-4|PAIRB_HUMAN Iso19,47Double-stranded RNA-binding protein Staufen homolog 1STAU1 sp|O95793-2|STAU1_HUMAN Isoform Short of Double-stranded RNA-binding protein Staufen homolog 1 OS=Homo sapiens GN=STAU1;sp|O95793|STAU1_HUMAN Double-stranded RNA-binding protein Staufen homolog 1 OS=Homo sapiens GN=STAU1 PE=1 SV=2;tr|Q5JW30|Q5JW30_HUMAN Do19,47Plakophilin-2 PKP2 sp|Q99959-2|PKP2_HUMAN Isoform 1 of Plakophilin-2 OS=Homo sapiens GN=PKP2;sp|Q99959|PKP2_HUMAN Plakophilin-2 OS=Homo sapiens GN=PKP2 PE=1 SV=219,4540S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2;40S ribosomal protein S4, Y isoform 1RPS4X;RPS4Y2;RPS4Y1sp|P62701|RS4X_HUMAN 40S ribosomal protein S4, X isoform OS=Homo sapiens GN=RPS4X PE=1 SV=2;sp|Q8TD47|RS4Y2_HUMAN 40S ribosomal protein S4, Y isoform 2 OS=Homo sapiens GN=RPS4Y2 PE=2 SV=3;tr|C9JEH7|C9JEH7_HUMAN 40S ribosomal protein S4, Y isoform 1 (Fragme19,36Transducin beta-like protein 3 TBL3 tr|J3KNP2|J3KNP2_HUMAN Transducin beta-like protein 3 (Fragment) OS=Homo sapiens GN=TBL3 PE=4 SV=1;sp|Q12788|TBL3_HUMAN Transducin beta-like protein 3 OS=Homo sapiens GN=TBL3 PE=1 SV=219,33Uncharacterized protein C7orf50 C7orf50 tr|C9JQV0|C9JQV0_HUMAN Uncharacterized protein C7orf50 (Fragment) OS=Homo sapiens GN=C7orf50 PE=2 SV=1;sp|Q9BRJ6|CG050_HUMAN Uncharacterized protein C7orf50 OS=Homo sapiens GN=C7orf50 PE=1 SV=119,08Negative elongation factor C/D TH1L;NELFCD tr|H0UI80|H0UI80_HUMAN Negative elongation factor C/D OS=Homo sapiens GN=TH1L PE=2 SV=1;sp|Q8IXH7-4|NELFD_HUMAN Isoform NELF-D of Negative elongation factor C/D OS=Homo sapiens GN=NELFCD;sp|Q8IXH7|NELFD_HUMAN Negative elongation factor C/D OS=Homo sapiens 19,0760S ribosomal protein L28 RPL28 tr|H0YLP6|H0YLP6_HUMAN 60S ribosomal protein L28 OS=Homo sapiens GN=RPL28 PE=2 SV=1;tr|H0YMF4|H0YMF4_HUMAN 60S ribosomal protein L28 OS=Homo sapiens GN=RPL28 PE=2 SV=1;tr|H0YKD8|H0YKD8_HUMAN 60S ribosomal protein L28 OS=Homo sapiens GN=RPL28 PE=2 SV=1;sp|P18,9960S ribosomal protein L29 RPL29 sp|P47914|RL29_HUMAN 60S ribosomal protein L29 OS=Homo sapiens GN=RPL29 PE=1 SV=218,9660S ribosomal protein L24 RPL24 tr|C9JXB8|C9JXB8_HUMAN 60S ribosomal protein L24 OS=Homo sapiens GN=RPL24 PE=2 SV=1;tr|C9JNW5|C9JNW5_HUMAN 60S ribosomal protein L24 OS=Homo sapiens GN=RPL24 PE=2 SV=1;sp|P83731|RL24_HUMAN 60S ribosomal protein L24 OS=Homo sapiens GN=RPL24 PE=1 SV=118,92Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processedGNB2L1 sp|P63244|GBLP_HUMAN Guanine nucleotide-binding protein subunit beta-2-like 1 OS=Homo sapiens GN=GNB2L1 PE=1 SV=3;tr|D6RHH4|D6RHH4_HUMAN Guanine nucleotide-binding protein subunit beta-2-like 1 OS=Homo sapiens GN=GNB2L1 PE=2 SV=1;tr|D6RAC2|D6RAC2_HUMAN Gua18,85Actin-like protein 6A ACTL6A sp|O96019-2|ACL6A_HUMAN Isoform 2 of Actin-like protein 6A OS=Homo sapiens GN=ACTL6A;sp|O96019|ACL6A_HUMAN Actin-like protein 6A OS=Homo sapiens GN=ACTL6A PE=1 SV=118,84Polyadenylate-binding protein;Polyadenylate-binding protein 4PABPC4 tr|B1ANR0|B1ANR0_HUMAN Poly(A) binding protein, cytoplasmic 4 (Inducible form), isoform CRA_e OS=Homo sapiens GN=PABPC4 PE=2 SV=1;sp|Q13310-2|PABP4_HUMAN Isoform 2 of Polyadenylate-binding protein 4 OS=Homo sapiens GN=PABPC4;sp|Q13310|PABP4_HUMAN Polyadeny18,71Eukaryotic translation initiation factor 3 subunit JEIF3J sp|O75822|EIF3J_HUMAN Eukaryotic translation initiation factor 3 subunit J OS=Homo sapiens GN=EIF3J PE=1 SV=2;tr|F5H425|F5H425_HUMAN Eukaryotic translation initiation factor 3 subunit J OS=Homo sapiens GN=EIF3J PE=2 SV=1;tr|H0YGJ7|H0YGJ7_HUMAN Eukaryotic t18,71Unconventional prefoldin RPB5 interactor 1 URI1 tr|F8W9T0|F8W9T0_HUMAN Unconventional prefoldin RPB5 interactor 1 OS=Homo sapiens GN=URI1 PE=2 SV=1;sp|O94763-3|RMP_HUMAN Isoform 3 of Unconventional prefoldin RPB5 interactor 1 OS=Homo sapiens GN=URI1;sp|O94763|RMP_HUMAN Unconventional prefoldin RPB5 inte18,6840S ribosomal protein S27;40S ribosomal protein S27-likeRPS27L tr|C9JLI6|C9JLI6_HUMAN 40S ribosomal protein S27 OS=Homo sapiens GN=RPS27L PE=2 SV=1;tr|H0YMV8|H0YMV8_HUMAN 40S ribosomal protein S27 OS=Homo sapiens GN=RPS27L PE=2 SV=1;sp|Q71UM5|RS27L_HUMAN 40S ribosomal protein S27-like OS=Homo sapiens GN=RPS27L PE=1 SV18,62Eukaryotic translation initiation factor 3 subunit IEIF3I sp|Q13347|EIF3I_HUMAN Eukaryotic translation initiation factor 3 subunit I OS=Homo sapiens GN=EIF3I PE=1 SV=118,25Caprin-1 CAPRIN1 sp|Q14444-2|CAPR1_HUMAN Isoform 2 of Caprin-1 OS=Homo sapiens GN=CAPRIN1;sp|Q14444|CAPR1_HUMAN Caprin-1 OS=Homo sapiens GN=CAPRIN1 PE=1 SV=2;tr|G3V153|G3V153_HUMAN Caprin-1 OS=Homo sapiens GN=CAPRIN1 PE=2 SV=1;tr|E9PLA9|E9PLA9_HUMAN Caprin-1 (Fragment) OS=18,2460S ribosomal protein L10a RPL10A sp|P62906|RL10A_HUMAN 60S ribosomal protein L10a OS=Homo sapiens GN=RPL10A PE=1 SV=218,14Heterogeneous nuclear ribonucleoprotein U HNRNPU sp|Q00839-2|HNRPU_HUMAN Isoform Short of Heterogeneous nuclear ribonucleoprotein U OS=Homo sapiens GN=HNRNPU18,08Eukaryotic translation initiation factor 3 subunit LEIF3L tr|B0QY89|B0QY89_HUMAN Eukaryotic translation initiation factor 3 subunit L OS=Homo sapiens GN=EIF3L PE=2 SV=1;sp|Q9Y262|EIF3L_HUMAN Eukaryotic translation initiation factor 3 subunit L OS=Homo sapiens GN=EIF3L PE=1 SV=1;sp|Q9Y262-2|EIF3L_HUMAN Isoform 2 o18,07Angiomotin-like protein 1 AMOTL1 sp|Q8IY63-2|AMOL1_HUMAN Isoform 2 of Angiomotin-like protein 1 OS=Homo sapiens GN=AMOTL1;sp|Q8IY63|AMOL1_HUMAN Angiomotin-like protein 1 OS=Homo sapiens GN=AMOTL1 PE=1 SV=118,00

Page 32: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Interferon-related developmental regulator 1 IFRD1 tr|C9JLG5|C9JLG5_HUMAN Interferon-related developmental regulator 1 (Fragment) OS=Homo sapiens GN=IFRD1 PE=2 SV=1;tr|C9JA65|C9JA65_HUMAN Interferon-related developmental regulator 1 OS=Homo sapiens GN=IFRD1 PE=2 SV=1;sp|O00458|IFRD1_HUMAN Interferon-relate17,99Uncharacterized protein C11orf98 C11orf98 tr|E9PLD3|E9PLD3_HUMAN Uncharacterized protein OS=Homo sapiens PE=4 SV=1;tr|E9PRG8|E9PRG8_HUMAN Uncharacterized protein C11orf48 OS=Homo sapiens GN=C11orf48 PE=2 SV=117,98SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1SMARCE1 tr|B4DGM3|B4DGM3_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 OS=Homo sapiens GN=SMARCE1 PE=2 SV=1;sp|Q969G3-6|SMCE1_HUMAN Isoform 6 of SWI/SNF-related matrix-associated actin-dependent regulator of ch17,95Helicase SKI2W SKIV2L tr|F5H7B0|F5H7B0_HUMAN Helicase SKI2W OS=Homo sapiens GN=SKIV2L PE=2 SV=1;sp|Q15477|SKIV2_HUMAN Helicase SKI2W OS=Homo sapiens GN=SKIV2L PE=1 SV=317,94Probable ATP-dependent RNA helicase DDX17DDX17 tr|H3BLZ8|H3BLZ8_HUMAN Probable ATP-dependent RNA helicase DDX17 OS=Homo sapiens GN=DDX17 PE=2 SV=1;sp|Q92841-1|DDX17_HUMAN Isoform 2 of Probable ATP-dependent RNA helicase DDX17 OS=Homo sapiens GN=DDX17;sp|Q92841-3|DDX17_HUMAN Isoform 4 of Probable ATP-de17,79Ubiquitin-associated protein 2-like UBAP2L sp|Q14157-4|UBP2L_HUMAN Isoform 4 of Ubiquitin-associated protein 2-like OS=Homo sapiens GN=UBAP2L;sp|Q14157-1|UBP2L_HUMAN Isoform 2 of Ubiquitin-associated protein 2-like OS=Homo sapiens GN=UBAP2L;tr|F8W726|F8W726_HUMAN Ubiquitin-associated protein 2-like17,58Pre-mRNA-splicing factor SPF27 BCAS2 sp|O75934|SPF27_HUMAN Pre-mRNA-splicing factor SPF27 OS=Homo sapiens GN=BCAS2 PE=1 SV=117,49Negative elongation factor B NELFB sp|Q8WX92|NELFB_HUMAN Negative elongation factor B OS=Homo sapiens GN=NELFB PE=1 SV=117,33Eukaryotic translation initiation factor 6 EIF6 sp|P56537|IF6_HUMAN Eukaryotic translation initiation factor 6 OS=Homo sapiens GN=EIF6 PE=1 SV=1;tr|B7ZBH1|B7ZBH1_HUMAN Eukaryotic translation initiation factor 6 (Fragment) OS=Homo sapiens GN=EIF6 PE=2 SV=117,32Probable ATP-dependent RNA helicase DDX5DDX5 tr|J3KTA4|J3KTA4_HUMAN Probable ATP-dependent RNA helicase DDX5 OS=Homo sapiens GN=DDX5 PE=2 SV=1;sp|P17844|DDX5_HUMAN Probable ATP-dependent RNA helicase DDX5 OS=Homo sapiens GN=DDX5 PE=1 SV=1;tr|B4DLW8|B4DLW8_HUMAN Probable ATP-dependent RNA helicase DDX17,30UPF0568 protein C14orf166 C14orf166 sp|Q9Y224|CN166_HUMAN UPF0568 protein C14orf166 OS=Homo sapiens GN=C14orf166 PE=1 SV=1;tr|G3V4C6|G3V4C6_HUMAN UPF0568 protein C14orf166 OS=Homo sapiens GN=C14orf166 PE=2 SV=117,20Transcription factor ETV6 ETV6 sp|P41212|ETV6_HUMAN Transcription factor ETV6 OS=Homo sapiens GN=ETV6 PE=1 SV=117,12Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2HNRNPA1;HNRNPA1L2tr|F8W6I7|F8W6I7_HUMAN Heterogeneous nuclear ribonucleoprotein A1 OS=Homo sapiens GN=HNRNPA1 PE=4 SV=2;sp|P09651-3|ROA1_HUMAN Isoform 2 of Heterogeneous nuclear ribonucleoprotein A1 OS=Homo sapiens GN=HNRNPA1;sp|P09651-2|ROA1_HUMAN Isoform A1-A of Heteroge16,96Dimethyladenosine transferase 1, mitochondrialTFB1M sp|Q8WVM0|TFB1M_HUMAN Dimethyladenosine transferase 1, mitochondrial OS=Homo sapiens GN=TFB1M PE=1 SV=116,95Eukaryotic translation initiation factor 3 subunit KEIF3K tr|K7ES31|K7ES31_HUMAN Eukaryotic translation initiation factor 3 subunit K OS=Homo sapiens GN=EIF3K PE=2 SV=1;tr|K7EMQ9|K7EMQ9_HUMAN Eukaryotic translation initiation factor 3 subunit K (Fragment) OS=Homo sapiens GN=EIF3K PE=2 SV=1;tr|K7ERF1|K7ERF1_HUMAN 16,79Roquin-1 RC3H1 sp|Q5TC82-2|RC3H1_HUMAN Isoform 2 of Roquin-1 OS=Homo sapiens GN=RC3H1;sp|Q5TC82|RC3H1_HUMAN Roquin-1 OS=Homo sapiens GN=RC3H1 PE=1 SV=116,49Eukaryotic translation initiation factor 3 subunit EEIF3E sp|P60228|EIF3E_HUMAN Eukaryotic translation initiation factor 3 subunit E OS=Homo sapiens GN=EIF3E PE=1 SV=1;tr|E5RGA2|E5RGA2_HUMAN Eukaryotic translation initiation factor 3 subunit E OS=Homo sapiens GN=EIF3E PE=2 SV=1;tr|H0YBR5|H0YBR5_HUMAN Eukaryotic t16,48Coiled-coil domain-containing protein 137 CCDC137 tr|I3L0U5|I3L0U5_HUMAN Coiled-coil domain-containing protein 137 (Fragment) OS=Homo sapiens GN=CCDC137 PE=2 SV=1;sp|Q6PK04|CC137_HUMAN Coiled-coil domain-containing protein 137 OS=Homo sapiens GN=CCDC137 PE=1 SV=116,43Cleavage and polyadenylation specificity factor subunit 3CPSF3 tr|G5E9W3|G5E9W3_HUMAN Cleavage and polyadenylation specific factor 3, 73kDa, isoform CRA_b OS=Homo sapiens GN=CPSF3 PE=2 SV=1;sp|Q9UKF6|CPSF3_HUMAN Cleavage and polyadenylation specificity factor subunit 3 OS=Homo sapiens GN=CPSF3 PE=1 SV=116,3040S ribosomal protein S21 RPS21 tr|Q8WVC2|Q8WVC2_HUMAN 40S ribosomal protein S21 OS=Homo sapiens GN=RPS21 PE=3 SV=1;sp|P63220|RS21_HUMAN 40S ribosomal protein S21 OS=Homo sapiens GN=RPS21 PE=1 SV=1;tr|Q9BYK1|Q9BYK1_HUMAN 40S ribosomal protein S21 OS=Homo sapiens GN=RPS21 PE=2 SV=116,28Angiomotin-like protein 2 AMOTL2 sp|Q9Y2J4|AMOL2_HUMAN Angiomotin-like protein 2 OS=Homo sapiens GN=AMOTL2 PE=1 SV=3;sp|Q9Y2J4-2|AMOL2_HUMAN Isoform 2 of Angiomotin-like protein 2 OS=Homo sapiens GN=AMOTL2;sp|Q9Y2J4-4|AMOL2_HUMAN Isoform 4 of Angiomotin-like protein 2 OS=Homo sapiens GN=A16,27Histone H1.2;Histone H1.3 HIST1H1C;HIST1H1Dsp|P16403|H12_HUMAN Histone H1.2 OS=Homo sapiens GN=HIST1H1C PE=1 SV=2;sp|P16402|H13_HUMAN Histone H1.3 OS=Homo sapiens GN=HIST1H1D PE=1 SV=216,23Prefoldin subunit 6 PFDN6 sp|O15212|PFD6_HUMAN Prefoldin subunit 6 OS=Homo sapiens GN=PFDN6 PE=1 SV=116,09Heterogeneous nuclear ribonucleoprotein A0HNRNPA0 sp|Q13151|ROA0_HUMAN Heterogeneous nuclear ribonucleoprotein A0 OS=Homo sapiens GN=HNRNPA0 PE=1 SV=115,96Poly(A) RNA polymerase, mitochondrial MTPAP sp|Q9NVV4|PAPD1_HUMAN Poly(A) RNA polymerase, mitochondrial OS=Homo sapiens GN=MTPAP PE=1 SV=1;sp|Q9NVV4-2|PAPD1_HUMAN Isoform 2 of Poly(A) RNA polymerase, mitochondrial OS=Homo sapiens GN=MTPAP15,63Nucleolar RNA helicase 2 DDX21 sp|Q9NR30|DDX21_HUMAN Nucleolar RNA helicase 2 OS=Homo sapiens GN=DDX21 PE=1 SV=5;sp|Q9NR30-2|DDX21_HUMAN Isoform 2 of Nucleolar RNA helicase 2 OS=Homo sapiens GN=DDX2115,49Eukaryotic translation initiation factor 3 subunit DEIF3D tr|B4DVY1|B4DVY1_HUMAN Eukaryotic translation initiation factor 3 subunit D OS=Homo sapiens GN=EIF3D PE=2 SV=1;sp|O15371|EIF3D_HUMAN Eukaryotic translation initiation factor 3 subunit D OS=Homo sapiens GN=EIF3D PE=1 SV=1;tr|B0QYA5|B0QYA5_HUMAN Eukaryotic t15,42Protein FAM98A FAM98A sp|Q8NCA5-2|FA98A_HUMAN Isoform 2 of Protein FAM98A OS=Homo sapiens GN=FAM98A;sp|Q8NCA5|FA98A_HUMAN Protein FAM98A OS=Homo sapiens GN=FAM98A PE=1 SV=1;tr|E9PH82|E9PH82_HUMAN Protein FAM98A OS=Homo sapiens GN=FAM98A PE=2 SV=1;tr|B4DT23|B4DT23_HUMAN Protein 15,25Splicing factor 3B subunit 3 SF3B3 sp|Q15393|SF3B3_HUMAN Splicing factor 3B subunit 3 OS=Homo sapiens GN=SF3B3 PE=1 SV=415,23Eukaryotic translation initiation factor 3 subunit GEIF3G tr|K7ER90|K7ER90_HUMAN Eukaryotic translation initiation factor 3 subunit G (Fragment) OS=Homo sapiens GN=EIF3G PE=2 SV=1;tr|K7EL20|K7EL20_HUMAN Eukaryotic translation initiation factor 3 subunit G (Fragment) OS=Homo sapiens GN=EIF3G PE=2 SV=1;sp|O75821|EI15,19Guanine nucleotide-binding protein-like 3 GNL3 sp|Q9BVP2-2|GNL3_HUMAN Isoform 2 of Guanine nucleotide-binding protein-like 3 OS=Homo sapiens GN=GNL3;sp|Q9BVP2|GNL3_HUMAN Guanine nucleotide-binding protein-like 3 OS=Homo sapiens GN=GNL3 PE=1 SV=215,04tRNA-splicing ligase RtcB homolog RTCB sp|Q9Y3I0|RTCB_HUMAN tRNA-splicing ligase RtcB homolog OS=Homo sapiens GN=RTCB PE=1 SV=114,98PIH1 domain-containing protein 1 PIH1D1 sp|Q9NWS0|PIHD1_HUMAN PIH1 domain-containing protein 1 OS=Homo sapiens GN=PIH1D1 PE=1 SV=1;tr|M0R3A4|M0R3A4_HUMAN PIH1 domain-containing protein 1 (Fragment) OS=Homo sapiens GN=PIH1D1 PE=4 SV=1;tr|M0QXD5|M0QXD5_HUMAN PIH1 domain-containing protein 1 (Fragm14,95Staphylococcal nuclease domain-containing protein 1SND1 sp|Q7KZF4|SND1_HUMAN Staphylococcal nuclease domain-containing protein 1 OS=Homo sapiens GN=SND1 PE=1 SV=114,93SWI/SNF complex subunit SMARCC1 SMARCC1 sp|Q92922|SMRC1_HUMAN SWI/SNF complex subunit SMARCC1 OS=Homo sapiens GN=SMARCC1 PE=1 SV=314,89SPATS2-like protein SPATS2L sp|Q9NUQ6-2|SPS2L_HUMAN Isoform 2 of SPATS2-like protein OS=Homo sapiens GN=SPATS2L;sp|Q9NUQ6|SPS2L_HUMAN SPATS2-like protein OS=Homo sapiens GN=SPATS2L PE=1 SV=2;tr|B4DRE6|B4DRE6_HUMAN SPATS2-like protein OS=Homo sapiens GN=SPATS2L PE=2 SV=1;tr|B4DT67|B4D14,83La-related protein 4 LARP4 tr|Q96J85|Q96J85_HUMAN C-Mpl binding protein OS=Homo sapiens GN=LARP4 PE=2 SV=1;sp|Q71RC2-7|LARP4_HUMAN Isoform 7 of La-related protein 4 OS=Homo sapiens GN=LARP4;sp|Q71RC2-2|LARP4_HUMAN Isoform 2 of La-related protein 4 OS=Homo sapiens GN=LARP4;sp|Q71RC2-14,75Pre-mRNA 3-end-processing factor FIP1 FIP1L1 sp|Q6UN15-5|FIP1_HUMAN Isoform 5 of Pre-mRNA 3-end-processing factor FIP1 OS=Homo sapiens GN=FIP1L1;sp|Q6UN15|FIP1_HUMAN Pre-mRNA 3-end-processing factor FIP1 OS=Homo sapiens GN=FIP1L1 PE=1 SV=1;sp|Q6UN15-4|FIP1_HUMAN Isoform 4 of Pre-mRNA 3-end-process14,65Coiled-coil domain-containing protein 124 CCDC124 sp|Q96CT7|CC124_HUMAN Coiled-coil domain-containing protein 124 OS=Homo sapiens GN=CCDC124 PE=1 SV=1;tr|M0R2F5|M0R2F5_HUMAN Coiled-coil domain-containing protein 124 (Fragment) OS=Homo sapiens GN=CCDC124 PE=2 SV=114,63Splicing factor 3B subunit 4 SF3B4 sp|Q15427|SF3B4_HUMAN Splicing factor 3B subunit 4 OS=Homo sapiens GN=SF3B4 PE=1 SV=114,54Galectin-3-binding protein LGALS3BP sp|Q08380|LG3BP_HUMAN Galectin-3-binding protein OS=Homo sapiens GN=LGALS3BP PE=1 SV=114,49Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1PLOD1 sp|Q02809|PLOD1_HUMAN Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 OS=Homo sapiens GN=PLOD1 PE=1 SV=2;tr|B4DR87|B4DR87_HUMAN Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 OS=Homo sapiens GN=PLOD1 PE=2 SV=114,38Nuclear cap-binding protein subunit 2 NCBP2 sp|P52298|NCBP2_HUMAN Nuclear cap-binding protein subunit 2 OS=Homo sapiens GN=NCBP2 PE=1 SV=1;tr|C9JQX9|C9JQX9_HUMAN Nuclear cap-binding protein subunit 2 (Fragment) OS=Homo sapiens GN=NCBP2 PE=2 SV=1;tr|B3KSB0|B3KSB0_HUMAN Nuclear cap binding protein sub14,33Putative ATP-dependent RNA helicase DHX30DHX30 tr|H7BXY3|H7BXY3_HUMAN Putative ATP-dependent RNA helicase DHX30 OS=Homo sapiens GN=DHX30 PE=2 SV=1;sp|Q7L2E3-3|DHX30_HUMAN Isoform 3 of Putative ATP-dependent RNA helicase DHX30 OS=Homo sapiens GN=DHX30;sp|Q7L2E3|DHX30_HUMAN Putative ATP-dependent RNA hel14,29Eukaryotic translation initiation factor 5B EIF5B sp|O60841|IF2P_HUMAN Eukaryotic translation initiation factor 5B OS=Homo sapiens GN=EIF5B PE=1 SV=414,28Mitogen-activated protein kinase kinase kinase MLTZAK sp|Q9NYL2|MLTK_HUMAN Mitogen-activated protein kinase kinase kinase MLT OS=Homo sapiens GN=ZAK PE=1 SV=3;sp|Q9NYL2-3|MLTK_HUMAN Isoform 3 of Mitogen-activated protein kinase kinase kinase MLT OS=Homo sapiens GN=ZAK;sp|Q9NYL2-2|MLTK_HUMAN Isoform 2 of Mitog14,27ATP-dependent RNA helicase DDX50 DDX50 sp|Q9BQ39|DDX50_HUMAN ATP-dependent RNA helicase DDX50 OS=Homo sapiens GN=DDX50 PE=1 SV=114,19Synaptonemal complex protein SC65 P3H4;LEPREL4 tr|K7ERA3|K7ERA3_HUMAN Synaptonemal complex protein SC65 (Fragment) OS=Homo sapiens GN=LEPREL4 PE=4 SV=1;sp|Q92791|SC65_HUMAN Synaptonemal complex protein SC65 OS=Homo sapiens GN=LEPREL4 PE=1 SV=114,16U3 small nucleolar ribonucleoprotein protein MPP10MPHOSPH10 sp|O00566|MPP10_HUMAN U3 small nucleolar ribonucleoprotein protein MPP10 OS=Homo sapiens GN=MPHOSPH10 PE=1 SV=2;tr|U3KQ48|U3KQ48_HUMAN U3 small nucleolar ribonucleoprotein protein MPP10 OS=Homo sapiens GN=MPHOSPH10 PE=4 SV=114,12Serine/threonine-protein phosphatase PGAM5, mitochondrialPGAM5 sp|Q96HS1-2|PGAM5_HUMAN Isoform 2 of Serine/threonine-protein phosphatase PGAM5, mitochondrial OS=Homo sapiens GN=PGAM5;sp|Q96HS1|PGAM5_HUMAN Serine/threonine-protein phosphatase PGAM5, mitochondrial OS=Homo sapiens GN=PGAM5 PE=1 SV=214,09Prohibitin PHB sp|P35232|PHB_HUMAN Prohibitin OS=Homo sapiens GN=PHB PE=1 SV=1;tr|C9JW96|C9JW96_HUMAN Prohibitin (Fragment) OS=Homo sapiens GN=PHB PE=2 SV=2;tr|C9JZ20|C9JZ20_HUMAN Prohibitin (Fragment) OS=Homo sapiens GN=PHB PE=2 SV=1;tr|E7ESE2|E7ESE2_HUMAN Prohibitin (F14,07Transcription elongation factor SPT6 SUPT6H sp|Q7KZ85|SPT6H_HUMAN Transcription elongation factor SPT6 OS=Homo sapiens GN=SUPT6H PE=1 SV=213,95Small nuclear ribonucleoprotein Sm D2 SNRPD2 tr|K7ERG4|K7ERG4_HUMAN Small nuclear ribonucleoprotein Sm D2 OS=Homo sapiens GN=SNRPD2 PE=2 SV=1;sp|P62316|SMD2_HUMAN Small nuclear ribonucleoprotein Sm D2 OS=Homo sapiens GN=SNRPD2 PE=1 SV=113,93Signal recognition particle 54 kDa protein SRP54 tr|G3V4F7|G3V4F7_HUMAN Signal recognition particle 54 kDa protein OS=Homo sapiens GN=SRP54 PE=2 SV=1;sp|P61011-2|SRP54_HUMAN Isoform 2 of Signal recognition particle 54 kDa protein OS=Homo sapiens GN=SRP54;sp|P61011|SRP54_HUMAN Signal recognition particle 13,89Serine/arginine-rich splicing factor 5 SRSF5 sp|Q13243-3|SRSF5_HUMAN Isoform SRP40-4 of Serine/arginine-rich splicing factor 5 OS=Homo sapiens GN=SRSF5;sp|Q13243|SRSF5_HUMAN Serine/arginine-rich splicing factor 5 OS=Homo sapiens GN=SRSF5 PE=1 SV=1;tr|B4DJK0|B4DJK0_HUMAN Serine/arginine-rich-splicing 13,88PDZ and LIM domain protein 7 PDLIM7 sp|Q9NR12|PDLI7_HUMAN PDZ and LIM domain protein 7 OS=Homo sapiens GN=PDLIM7 PE=1 SV=1;sp|Q9NR12-2|PDLI7_HUMAN Isoform 2 of PDZ and LIM domain protein 7 OS=Homo sapiens GN=PDLIM7;tr|D6RF83|D6RF83_HUMAN PDZ and LIM domain protein 7 (Fragment) OS=Homo sapien13,80

Page 33: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Splicing factor 45 RBM17 sp|Q96I25|SPF45_HUMAN Splicing factor 45 OS=Homo sapiens GN=RBM17 PE=1 SV=1;tr|Q5W011|Q5W011_HUMAN Splicing factor 45 (Fragment) OS=Homo sapiens GN=RBM17 PE=2 SV=1;tr|Q5W010|Q5W010_HUMAN Splicing factor 45 (Fragment) OS=Homo sapiens GN=RBM17 PE=2 SV=113,79Prefoldin subunit 2 PFDN2 sp|Q9UHV9|PFD2_HUMAN Prefoldin subunit 2 OS=Homo sapiens GN=PFDN2 PE=1 SV=113,71Zinc finger protein ubi-d4 DPF2 tr|J3KMZ8|J3KMZ8_HUMAN Zinc finger protein ubi-d4 OS=Homo sapiens GN=DPF2 PE=2 SV=1;sp|Q92785|REQU_HUMAN Zinc finger protein ubi-d4 OS=Homo sapiens GN=DPF2 PE=1 SV=2;tr|B4DT58|B4DT58_HUMAN Zinc finger protein ubi-d4 OS=Homo sapiens GN=DPF2 PE=2 SV=1;tr|E9P13,67Signal recognition particle subunit SRP72 SRP72 sp|O76094-2|SRP72_HUMAN Isoform 2 of Signal recognition particle subunit SRP72 OS=Homo sapiens GN=SRP72;sp|O76094|SRP72_HUMAN Signal recognition particle subunit SRP72 OS=Homo sapiens GN=SRP72 PE=1 SV=3;tr|D6RDY6|D6RDY6_HUMAN Signal recognition particle su13,66Ubiquitin carboxyl-terminal hydrolase 10 USP10 sp|Q14694|UBP10_HUMAN Ubiquitin carboxyl-terminal hydrolase 10 OS=Homo sapiens GN=USP10 PE=1 SV=2;sp|Q14694-3|UBP10_HUMAN Isoform 3 of Ubiquitin carboxyl-terminal hydrolase 10 OS=Homo sapiens GN=USP10;sp|Q14694-2|UBP10_HUMAN Isoform 2 of Ubiquitin carboxyl13,65Histone H1x H1FX sp|Q92522|H1X_HUMAN Histone H1x OS=Homo sapiens GN=H1FX PE=1 SV=113,62Exosome complex component MTR3 EXOSC6 sp|Q5RKV6|EXOS6_HUMAN Exosome complex component MTR3 OS=Homo sapiens GN=EXOSC6 PE=1 SV=113,54Enhancer of rudimentary homolog ERH sp|P84090|ERH_HUMAN Enhancer of rudimentary homolog OS=Homo sapiens GN=ERH PE=1 SV=1;tr|G3V279|G3V279_HUMAN Enhancer of rudimentary homolog OS=Homo sapiens GN=ERH PE=2 SV=113,4840S ribosomal protein S30 FAU tr|E9PR30|E9PR30_HUMAN 40S ribosomal protein S30 OS=Homo sapiens GN=FAU PE=2 SV=1;sp|P62861|RS30_HUMAN 40S ribosomal protein S30 OS=Homo sapiens GN=FAU PE=1 SV=113,46Probable rRNA-processing protein EBP2 EBNA1BP2 tr|H7C2Q8|H7C2Q8_HUMAN EBNA1 binding protein 2, isoform CRA_d OS=Homo sapiens GN=EBNA1BP2 PE=2 SV=1;sp|Q99848|EBP2_HUMAN Probable rRNA-processing protein EBP2 OS=Homo sapiens GN=EBNA1BP2 PE=1 SV=213,38RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processedRBMX sp|P38159|RBMX_HUMAN RNA-binding motif protein, X chromosome OS=Homo sapiens GN=RBMX PE=1 SV=3;sp|P38159-2|RBMX_HUMAN Isoform 2 of RNA-binding motif protein, X chromosome OS=Homo sapiens GN=RBMX;tr|H0Y6E7|H0Y6E7_HUMAN RNA-binding motif protein, X chromosom13,36NEDD4 family-interacting protein 1 NDFIP1 sp|Q9BT67|NFIP1_HUMAN NEDD4 family-interacting protein 1 OS=Homo sapiens GN=NDFIP1 PE=1 SV=113,17WD repeat-containing protein 61;WD repeat-containing protein 61, N-terminally processedWDR61 tr|H0YN81|H0YN81_HUMAN WD repeat-containing protein 61 (Fragment) OS=Homo sapiens GN=WDR61 PE=2 SV=1;sp|Q9GZS3|WDR61_HUMAN WD repeat-containing protein 61 OS=Homo sapiens GN=WDR61 PE=1 SV=1;tr|H0YMF9|H0YMF9_HUMAN WD repeat-containing protein 61 OS=Homo sap13,14Endothelial differentiation-related factor 1 EDF1 sp|O60869-2|EDF1_HUMAN Isoform 2 of Endothelial differentiation-related factor 1 OS=Homo sapiens GN=EDF1;sp|O60869|EDF1_HUMAN Endothelial differentiation-related factor 1 OS=Homo sapiens GN=EDF1 PE=1 SV=113,03Prohibitin-2 PHB2 tr|F5GY37|F5GY37_HUMAN Prohibitin-2 OS=Homo sapiens GN=PHB2 PE=2 SV=1;tr|J3KPX7|J3KPX7_HUMAN Prohibitin-2 OS=Homo sapiens GN=PHB2 PE=2 SV=1;sp|Q99623|PHB2_HUMAN Prohibitin-2 OS=Homo sapiens GN=PHB2 PE=1 SV=2;tr|F5H3X6|F5H3X6_HUMAN Prohibitin-2 (Fragment) O13,01Nucleolin NCL sp|P19338|NUCL_HUMAN Nucleolin OS=Homo sapiens GN=NCL PE=1 SV=3;tr|H7BY16|H7BY16_HUMAN Nucleolin (Fragment) OS=Homo sapiens GN=NCL PE=2 SV=113,00

ASNSD1 tr|L0R819|L0R819_HUMAN Alternative protein ASNSD1 OS=Homo sapiens GN=ASNSD1 PE=4 SV=1;tr|U3KQP1|U3KQP1_HUMAN Asparagine synthetase domain-containing protein 1 (Fragment) OS=Homo sapiens GN=ASNSD1 PE=4 SV=112,99ELAV-like protein 1 ELAVL1 sp|Q15717|ELAV1_HUMAN ELAV-like protein 1 OS=Homo sapiens GN=ELAVL1 PE=1 SV=2;tr|B4DVB8|B4DVB8_HUMAN ELAV-like protein 1 OS=Homo sapiens GN=ELAVL1 PE=2 SV=1;tr|M0QZR9|M0QZR9_HUMAN ELAV-like protein 1 OS=Homo sapiens GN=ELAVL1 PE=2 SV=112,81Pre-mRNA-processing factor 19 PRPF19 sp|Q9UMS4|PRP19_HUMAN Pre-mRNA-processing factor 19 OS=Homo sapiens GN=PRPF19 PE=1 SV=112,72Transcription elongation factor B polypeptide 2TCEB2 tr|B8ZZU8|B8ZZU8_HUMAN Transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B), isoform CRA_b OS=Homo sapiens GN=TCEB2 PE=2 SV=1;tr|I3L0M9|I3L0M9_HUMAN Transcription elongation factor B polypeptide 2 (Fragment) OS=Homo sapiens GN=TCEB2 P12,69WW domain-binding protein 2 WBP2 tr|K7EIJ0|K7EIJ0_HUMAN WW domain-binding protein 2 (Fragment) OS=Homo sapiens GN=WBP2 PE=2 SV=1;tr|K7ENL2|K7ENL2_HUMAN WW domain-binding protein 2 OS=Homo sapiens GN=WBP2 PE=2 SV=1;tr|A6NG10|A6NG10_HUMAN WW domain-binding protein 2 OS=Homo sapiens GN=WBP2 12,66Eukaryotic initiation factor 4A-I;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processedEIF4A1;EIF4A2 sp|P60842|IF4A1_HUMAN Eukaryotic initiation factor 4A-I OS=Homo sapiens GN=EIF4A1 PE=1 SV=1;tr|J3KT12|J3KT12_HUMAN Eukaryotic initiation factor 4A-I OS=Homo sapiens GN=EIF4A1 PE=2 SV=1;sp|P60842-2|IF4A1_HUMAN Isoform 2 of Eukaryotic initiation factor 4A-I 12,64Ubiquitin carboxyl-terminal hydrolase 24 USP24 sp|Q9UPU5|UBP24_HUMAN Ubiquitin carboxyl-terminal hydrolase 24 OS=Homo sapiens GN=USP24 PE=1 SV=3;tr|B7WPF4|B7WPF4_HUMAN Ubiquitin carboxyl-terminal hydrolase OS=Homo sapiens GN=USP24 PE=2 SV=212,63GPN-loop GTPase 3 GPN3 sp|Q9UHW5|GPN3_HUMAN GPN-loop GTPase 3 OS=Homo sapiens GN=GPN3 PE=1 SV=2;sp|Q9UHW5-2|GPN3_HUMAN Isoform 2 of GPN-loop GTPase 3 OS=Homo sapiens GN=GPN3;tr|S4R3M7|S4R3M7_HUMAN GPN-loop GTPase 3 (Fragment) OS=Homo sapiens GN=GPN3 PE=4 SV=1;tr|H0YI19|H0YI19_HU12,42Putative 40S ribosomal protein S26-like 1;40S ribosomal protein S26RPS26P11;RPS26 sp|Q5JNZ5|RS26L_HUMAN Putative 40S ribosomal protein S26-like 1 OS=Homo sapiens GN=RPS26P11 PE=5 SV=1;sp|P62854|RS26_HUMAN 40S ribosomal protein S26 OS=Homo sapiens GN=RPS26 PE=1 SV=312,38Integral membrane protein DGCR2/IDD DKFZp686I1730;DGCR2tr|Q5CZ70|Q5CZ70_HUMAN Integral membrane protein DGCR2/IDD OS=Homo sapiens GN=DKFZp686I1730 PE=2 SV=1;sp|P98153-2|IDD_HUMAN Isoform 2 of Integral membrane protein DGCR2/IDD OS=Homo sapiens GN=DGCR2;sp|P98153|IDD_HUMAN Integral membrane protein DGCR2/IDD OS12,28SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1SMARCD1 sp|Q96GM5|SMRD1_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 OS=Homo sapiens GN=SMARCD1 PE=1 SV=2;sp|Q96GM5-2|SMRD1_HUMAN Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chr12,26Interferon-inducible double-stranded RNA-dependent protein kinase activator APRKRA sp|O75569-3|PRKRA_HUMAN Isoform 3 of Interferon-inducible double-stranded RNA-dependent protein kinase activator A OS=Homo sapiens GN=PRKRA;sp|O75569-2|PRKRA_HUMAN Isoform 2 of Interferon-inducible double-stranded RNA-dependent protein kinase activator A O12,23Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15DHX15 sp|O43143|DHX15_HUMAN Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 OS=Homo sapiens GN=DHX15 PE=1 SV=212,10Glutamate-rich WD repeat-containing protein 1GRWD1 sp|Q9BQ67|GRWD1_HUMAN Glutamate-rich WD repeat-containing protein 1 OS=Homo sapiens GN=GRWD1 PE=1 SV=112,09Heterogeneous nuclear ribonucleoproteins C1/C2HNRNPC tr|G3V4W0|G3V4W0_HUMAN Heterogeneous nuclear ribonucleoproteins C1/C2 (Fragment) OS=Homo sapiens GN=HNRNPC PE=2 SV=1;tr|B4DY08|B4DY08_HUMAN Heterogeneous nuclear ribonucleoproteins C1/C2 OS=Homo sapiens GN=HNRNPC PE=2 SV=1;tr|G3V4C1|G3V4C1_HUMAN Heterogene12,08RNA-binding protein 34 RBM34 tr|A2A2V2|A2A2V2_HUMAN RNA-binding protein 34 (Fragment) OS=Homo sapiens GN=RBM34 PE=2 SV=1;sp|P42696|RBM34_HUMAN RNA-binding protein 34 OS=Homo sapiens GN=RBM34 PE=1 SV=2;tr|Q5TCT4|Q5TCT4_HUMAN RNA-binding protein 34 (Fragment) OS=Homo sapiens GN=RBM34 PE11,99Zinc finger protein 638 ZNF638 sp|Q14966-4|ZN638_HUMAN Isoform 4 of Zinc finger protein 638 OS=Homo sapiens GN=ZNF638;sp|Q14966-3|ZN638_HUMAN Isoform 3 of Zinc finger protein 638 OS=Homo sapiens GN=ZNF638;sp|Q14966|ZN638_HUMAN Zinc finger protein 638 OS=Homo sapiens GN=ZNF638 PE=1 SV=2;11,85Serine/threonine-protein phosphatase 1 regulatory subunit 10PPP1R10 sp|Q96QC0|PP1RA_HUMAN Serine/threonine-protein phosphatase 1 regulatory subunit 10 OS=Homo sapiens GN=PPP1R10 PE=1 SV=111,83La-related protein 1 LARP1 sp|Q6PKG0|LARP1_HUMAN La-related protein 1 OS=Homo sapiens GN=LARP1 PE=1 SV=2;sp|Q6PKG0-3|LARP1_HUMAN Isoform 2 of La-related protein 1 OS=Homo sapiens GN=LARP111,72Protein SDA1 homolog SDAD1 sp|Q9NVU7|SDA1_HUMAN Protein SDA1 homolog OS=Homo sapiens GN=SDAD1 PE=1 SV=3;tr|E7EW05|E7EW05_HUMAN Protein SDA1 homolog OS=Homo sapiens GN=SDAD1 PE=2 SV=1;sp|Q9NVU7-2|SDA1_HUMAN Isoform 2 of Protein SDA1 homolog OS=Homo sapiens GN=SDAD111,71Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1NMNAT1 sp|Q9HAN9|NMNA1_HUMAN Nicotinamide mononucleotide adenylyltransferase 1 OS=Homo sapiens GN=NMNAT1 PE=1 SV=111,67MKI67 FHA domain-interacting nucleolar phosphoproteinNIFK sp|Q9BYG3|MK67I_HUMAN MKI67 FHA domain-interacting nucleolar phosphoprotein OS=Homo sapiens GN=NIFK PE=1 SV=1;tr|C9J808|C9J808_HUMAN MKI67 FHA domain-interacting nucleolar phosphoprotein (Fragment) OS=Homo sapiens GN=NIFK PE=2 SV=111,63DNA topoisomerase 2-alpha TOP2A sp|P11388|TOP2A_HUMAN DNA topoisomerase 2-alpha OS=Homo sapiens GN=TOP2A PE=1 SV=3;sp|P11388-2|TOP2A_HUMAN Isoform 2 of DNA topoisomerase 2-alpha OS=Homo sapiens GN=TOP2A;sp|P11388-3|TOP2A_HUMAN Isoform 3 of DNA topoisomerase 2-alpha OS=Homo sapiens GN=TOP11,57Non-POU domain-containing octamer-binding proteinNONO sp|Q15233-2|NONO_HUMAN Isoform 2 of Non-POU domain-containing octamer-binding protein OS=Homo sapiens GN=NONO;sp|Q15233|NONO_HUMAN Non-POU domain-containing octamer-binding protein OS=Homo sapiens GN=NONO PE=1 SV=4;tr|H7C367|H7C367_HUMAN Non-POU domain-con11,52Probable global transcription activator SNF2L2SMARCA2 sp|P51531-2|SMCA2_HUMAN Isoform Short of Probable global transcription activator SNF2L2 OS=Homo sapiens GN=SMARCA2;sp|P51531|SMCA2_HUMAN Probable global transcription activator SNF2L2 OS=Homo sapiens GN=SMARCA2 PE=1 SV=211,44Cleavage and polyadenylation specificity factor subunit 2CPSF2 sp|Q9P2I0|CPSF2_HUMAN Cleavage and polyadenylation specificity factor subunit 2 OS=Homo sapiens GN=CPSF2 PE=1 SV=211,35Insulin-like growth factor 2 mRNA-binding protein 2IGF2BP2 tr|F8W930|F8W930_HUMAN Insulin-like growth factor 2 mRNA-binding protein 2 OS=Homo sapiens GN=IGF2BP2 PE=2 SV=1;sp|Q9Y6M1-1|IF2B2_HUMAN Isoform 2 of Insulin-like growth factor 2 mRNA-binding protein 2 OS=Homo sapiens GN=IGF2BP2;sp|Q9Y6M1|IF2B2_HUMAN Insuli11,34Heterogeneous nuclear ribonucleoprotein Q SYNCRIP sp|O60506-2|HNRPQ_HUMAN Isoform 2 of Heterogeneous nuclear ribonucleoprotein Q OS=Homo sapiens GN=SYNCRIP;sp|O60506|HNRPQ_HUMAN Heterogeneous nuclear ribonucleoprotein Q OS=Homo sapiens GN=SYNCRIP PE=1 SV=2;sp|O60506-4|HNRPQ_HUMAN Isoform 4 of Heterogeneou11,312,4-dienoyl-CoA reductase, mitochondrial DECR1 tr|B7Z6B8|B7Z6B8_HUMAN 2,4-dienoyl-CoA reductase, mitochondrial OS=Homo sapiens GN=DECR1 PE=2 SV=1;sp|Q16698|DECR_HUMAN 2,4-dienoyl-CoA reductase, mitochondrial OS=Homo sapiens GN=DECR1 PE=1 SV=1;tr|E5RJG7|E5RJG7_HUMAN 2,4-dienoyl-CoA reductase, mitochondr11,28NF-kappa-B-repressing factor NKRF sp|O15226|NKRF_HUMAN NF-kappa-B-repressing factor OS=Homo sapiens GN=NKRF PE=1 SV=2;sp|O15226-2|NKRF_HUMAN Isoform 2 of NF-kappa-B-repressing factor OS=Homo sapiens GN=NKRF11,28Insulin-like growth factor 2 mRNA-binding protein 1IGF2BP1 sp|Q9NZI8|IF2B1_HUMAN Insulin-like growth factor 2 mRNA-binding protein 1 OS=Homo sapiens GN=IGF2BP1 PE=1 SV=2;sp|Q9NZI8-2|IF2B1_HUMAN Isoform 2 of Insulin-like growth factor 2 mRNA-binding protein 1 OS=Homo sapiens GN=IGF2BP111,27Transcription factor BTF3 BTF3 tr|H0Y9Y1|H0Y9Y1_HUMAN Transcription factor BTF3 (Fragment) OS=Homo sapiens GN=BTF3 PE=2 SV=2;tr|D6RDG3|D6RDG3_HUMAN Transcription factor BTF3 (Fragment) OS=Homo sapiens GN=BTF3 PE=2 SV=2;sp|P20290-2|BTF3_HUMAN Isoform 2 of Transcription factor BTF3 OS=Hom11,23Putative ATP-dependent RNA helicase DHX57DHX57 sp|Q6P158|DHX57_HUMAN Putative ATP-dependent RNA helicase DHX57 OS=Homo sapiens GN=DHX57 PE=1 SV=211,15Protein transport protein Sec61 subunit beta SEC61B sp|P60468|SC61B_HUMAN Protein transport protein Sec61 subunit beta OS=Homo sapiens GN=SEC61B PE=1 SV=211,06Ribosome-binding protein 1 RRBP1 sp|Q9P2E9|RRBP1_HUMAN Ribosome-binding protein 1 OS=Homo sapiens GN=RRBP1 PE=1 SV=4;sp|Q9P2E9-2|RRBP1_HUMAN Isoform 1 of Ribosome-binding protein 1 OS=Homo sapiens GN=RRBP1;sp|Q9P2E9-3|RRBP1_HUMAN Isoform 2 of Ribosome-binding protein 1 OS=Homo sapiens GN=10,99Heterogeneous nuclear ribonucleoprotein R HNRNPR sp|O43390-3|HNRPR_HUMAN Isoform 3 of Heterogeneous nuclear ribonucleoprotein R OS=Homo sapiens GN=HNRNPR;sp|O43390|HNRPR_HUMAN Heterogeneous nuclear ribonucleoprotein R OS=Homo sapiens GN=HNRNPR PE=1 SV=1;sp|O43390-2|HNRPR_HUMAN Isoform 2 of Heterogeneous 10,98Exosome complex component RRP41 EXOSC4 sp|Q9NPD3|EXOS4_HUMAN Exosome complex component RRP41 OS=Homo sapiens GN=EXOSC4 PE=1 SV=3;tr|E9PPI9|E9PPI9_HUMAN Exosome complex component RRP41 OS=Homo sapiens GN=EXOSC4 PE=2 SV=1;tr|E9PI41|E9PI41_HUMAN Exosome complex component RRP41 (Fragment) OS=Homo s10,97Ataxin-2 ATXN2 tr|H0YH87|H0YH87_HUMAN Ataxin-2 (Fragment) OS=Homo sapiens GN=ATXN2 PE=4 SV=1;tr|F8WB06|F8WB06_HUMAN Ataxin-2 OS=Homo sapiens GN=ATXN2 PE=2 SV=1;tr|F8VQP2|F8VQP2_HUMAN Ataxin-2 OS=Homo sapiens GN=ATXN2 PE=2 SV=1;tr|V9GY86|V9GY86_HUMAN Ataxin-2 OS=Homo sapi10,93SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1SMARCB1 sp|Q12824|SNF5_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 OS=Homo sapiens GN=SMARCB1 PE=1 SV=2;tr|B5MCL5|B5MCL5_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamil10,83Eukaryotic translation initiation factor 4 gamma 1EIF4G1 tr|E7EX73|E7EX73_HUMAN Eukaryotic translation initiation factor 4 gamma 1 OS=Homo sapiens GN=EIF4G1 PE=2 SV=1;tr|E9PGM1|E9PGM1_HUMAN Eukaryotic translation initiation factor 4 gamma 1 OS=Homo sapiens GN=EIF4G1 PE=2 SV=1;tr|E7EUU4|E7EUU4_HUMAN Eukaryotic tr10,77

Page 34: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Cyclin-dependent kinase 9 CDK9 sp|P50750|CDK9_HUMAN Cyclin-dependent kinase 9 OS=Homo sapiens GN=CDK9 PE=1 SV=3;sp|P50750-2|CDK9_HUMAN Isoform 2 of Cyclin-dependent kinase 9 OS=Homo sapiens GN=CDK910,72tRNA (cytosine(34)-C(5))-methyltransferase NSUN2 sp|Q08J23-2|NSUN2_HUMAN Isoform 2 of tRNA (cytosine(34)-C(5))-methyltransferase OS=Homo sapiens GN=NSUN2;sp|Q08J23|NSUN2_HUMAN tRNA (cytosine(34)-C(5))-methyltransferase OS=Homo sapiens GN=NSUN2 PE=1 SV=2;sp|Q08J23-3|NSUN2_HUMAN Isoform 3 of tRNA (cytosine10,57DNA topoisomerase 1 TOP1 sp|P11387|TOP1_HUMAN DNA topoisomerase 1 OS=Homo sapiens GN=TOP1 PE=1 SV=210,54U2 small nuclear ribonucleoprotein B SNRPB2 sp|P08579|RU2B_HUMAN U2 small nuclear ribonucleoprotein B OS=Homo sapiens GN=SNRPB2 PE=1 SV=110,46Target of EGR1 protein 1 TOE1 sp|Q96GM8|TOE1_HUMAN Target of EGR1 protein 1 OS=Homo sapiens GN=TOE1 PE=1 SV=1;tr|B4DEM6|B4DEM6_HUMAN Target of EGR1 protein 1 OS=Homo sapiens GN=TOE1 PE=2 SV=110,43AT-rich interactive domain-containing protein 1AARID1A sp|O14497|ARI1A_HUMAN AT-rich interactive domain-containing protein 1A OS=Homo sapiens GN=ARID1A PE=1 SV=3;sp|O14497-3|ARI1A_HUMAN Isoform 3 of AT-rich interactive domain-containing protein 1A OS=Homo sapiens GN=ARID1A;sp|O14497-2|ARI1A_HUMAN Isoform 2 of 10,37Signal recognition particle 14 kDa protein SRP14 sp|P37108|SRP14_HUMAN Signal recognition particle 14 kDa protein OS=Homo sapiens GN=SRP14 PE=1 SV=2;tr|H0YLA2|H0YLA2_HUMAN Signal recognition particle 14 kDa protein OS=Homo sapiens GN=SRP14 PE=2 SV=110,35ATP-binding cassette sub-family F member 1 ABCF1 sp|Q8NE71-2|ABCF1_HUMAN Isoform 2 of ATP-binding cassette sub-family F member 1 OS=Homo sapiens GN=ABCF1;sp|Q8NE71|ABCF1_HUMAN ATP-binding cassette sub-family F member 1 OS=Homo sapiens GN=ABCF1 PE=1 SV=2;tr|H0YGW7|H0YGW7_HUMAN ATP-binding cassette sub-fam10,35Lysine--tRNA ligase KARS sp|Q15046|SYK_HUMAN Lysine--tRNA ligase OS=Homo sapiens GN=KARS PE=1 SV=3;sp|Q15046-2|SYK_HUMAN Isoform Mitochondrial of Lysine--tRNA ligase OS=Homo sapiens GN=KARS10,34Cytoskeleton-associated protein 4 CKAP4 sp|Q07065|CKAP4_HUMAN Cytoskeleton-associated protein 4 OS=Homo sapiens GN=CKAP4 PE=1 SV=210,31Heterochromatin protein 1-binding protein 3 HP1BP3 sp|Q5SSJ5|HP1B3_HUMAN Heterochromatin protein 1-binding protein 3 OS=Homo sapiens GN=HP1BP3 PE=1 SV=1;sp|Q5SSJ5-2|HP1B3_HUMAN Isoform 2 of Heterochromatin protein 1-binding protein 3 OS=Homo sapiens GN=HP1BP3;tr|B0QZK4|B0QZK4_HUMAN Heterochromatin protein 10,31Microprocessor complex subunit DGCR8 DGCR8 sp|Q8WYQ5-3|DGCR8_HUMAN Isoform 3 of Microprocessor complex subunit DGCR8 OS=Homo sapiens GN=DGCR8;sp|Q8WYQ5|DGCR8_HUMAN Microprocessor complex subunit DGCR8 OS=Homo sapiens GN=DGCR8 PE=1 SV=110,29Nascent polypeptide-associated complex subunit alpha;Nascent polypeptide-associated complex subunit alpha, muscle-specific formNACA tr|F8VZJ2|F8VZJ2_HUMAN Nascent polypeptide-associated complex subunit alpha, muscle-specific form OS=Homo sapiens GN=NACA PE=2 SV=1;tr|F8W0W4|F8W0W4_HUMAN Nascent polypeptide-associated complex subunit alpha, muscle-specific form (Fragment) OS=Homo sapiens10,27Zinc finger protein 622 ZNF622 sp|Q969S3|ZN622_HUMAN Zinc finger protein 622 OS=Homo sapiens GN=ZNF622 PE=1 SV=110,26Sphingosine-1-phosphate lyase 1 SGPL1 sp|O95470|SGPL1_HUMAN Sphingosine-1-phosphate lyase 1 OS=Homo sapiens GN=SGPL1 PE=1 SV=310,21ATP-dependent RNA helicase DHX29 DHX29 sp|Q7Z478|DHX29_HUMAN ATP-dependent RNA helicase DHX29 OS=Homo sapiens GN=DHX29 PE=1 SV=210,20GPN-loop GTPase 1 GPN1 sp|Q9HCN4-4|GPN1_HUMAN Isoform 4 of GPN-loop GTPase 1 OS=Homo sapiens GN=GPN1;sp|Q9HCN4|GPN1_HUMAN GPN-loop GTPase 1 OS=Homo sapiens GN=GPN1 PE=1 SV=1;tr|B4DQM4|B4DQM4_HUMAN GPN-loop GTPase 1 OS=Homo sapiens GN=GPN1 PE=2 SV=1;sp|Q9HCN4-3|GPN1_HUMAN Isoform10,11RNA polymerase II subunit A C-terminal domain phosphataseCTDP1 sp|Q9Y5B0|CTDP1_HUMAN RNA polymerase II subunit A C-terminal domain phosphatase OS=Homo sapiens GN=CTDP1 PE=1 SV=3;sp|Q9Y5B0-4|CTDP1_HUMAN Isoform 4 of RNA polymerase II subunit A C-terminal domain phosphatase OS=Homo sapiens GN=CTDP1;tr|K7EJD2|K7EJD2_HUMA10,01Serine/arginine-rich splicing factor 3 SRSF3 tr|B4E241|B4E241_HUMAN Serine/arginine-rich-splicing factor 3 OS=Homo sapiens GN=SFRS3 PE=2 SV=1;sp|P84103|SRSF3_HUMAN Serine/arginine-rich splicing factor 3 OS=Homo sapiens GN=SRSF3 PE=1 SV=19,98Pleiotropic regulator 1 PLRG1 tr|A8MW61|A8MW61_HUMAN Pleiotropic regulator 1 OS=Homo sapiens GN=PLRG1 PE=2 SV=1;sp|O43660-2|PLRG1_HUMAN Isoform 2 of Pleiotropic regulator 1 OS=Homo sapiens GN=PLRG1;sp|O43660|PLRG1_HUMAN Pleiotropic regulator 1 OS=Homo sapiens GN=PLRG1 PE=1 SV=19,91Small nuclear ribonucleoprotein Sm D3 SNRPD3 tr|B4DJP7|B4DJP7_HUMAN Small nuclear ribonucleoprotein Sm D3 OS=Homo sapiens GN=SNRPD3 PE=2 SV=1;sp|P62318|SMD3_HUMAN Small nuclear ribonucleoprotein Sm D3 OS=Homo sapiens GN=SNRPD3 PE=1 SV=19,84Heterogeneous nuclear ribonucleoprotein A3HNRNPA3 sp|P51991|ROA3_HUMAN Heterogeneous nuclear ribonucleoprotein A3 OS=Homo sapiens GN=HNRNPA3 PE=1 SV=2;sp|P51991-2|ROA3_HUMAN Isoform 2 of Heterogeneous nuclear ribonucleoprotein A3 OS=Homo sapiens GN=HNRNPA39,81Histone H1.0;Histone H1.0, N-terminally processedH1F0 sp|P07305|H10_HUMAN Histone H1.0 OS=Homo sapiens GN=H1F0 PE=1 SV=3;sp|P07305-2|H10_HUMAN Isoform 2 of Histone H1.0 OS=Homo sapiens GN=H1F09,81Heterogeneous nuclear ribonucleoproteins A2/B1HNRNPA2B1 sp|P22626|ROA2_HUMAN Heterogeneous nuclear ribonucleoproteins A2/B1 OS=Homo sapiens GN=HNRNPA2B1 PE=1 SV=2;sp|P22626-2|ROA2_HUMAN Isoform A2 of Heterogeneous nuclear ribonucleoproteins A2/B1 OS=Homo sapiens GN=HNRNPA2B19,80Probable ATP-dependent RNA helicase DDX27DDX27 sp|Q96GQ7|DDX27_HUMAN Probable ATP-dependent RNA helicase DDX27 OS=Homo sapiens GN=DDX27 PE=1 SV=29,71InaD-like protein INADL sp|Q8NI35|INADL_HUMAN InaD-like protein OS=Homo sapiens GN=INADL PE=1 SV=3;sp|Q8NI35-4|INADL_HUMAN Isoform 4 of InaD-like protein OS=Homo sapiens GN=INADL;sp|Q8NI35-3|INADL_HUMAN Isoform 3 of InaD-like protein OS=Homo sapiens GN=INADL;sp|Q8NI35-2|INADL_HUM9,71THO complex subunit 4 ALYREF tr|E9PB61|E9PB61_HUMAN THO complex subunit 4 OS=Homo sapiens GN=ALYREF PE=2 SV=1;sp|Q86V81|THOC4_HUMAN THO complex subunit 4 OS=Homo sapiens GN=ALYREF PE=1 SV=39,65Leucine-rich repeat-containing protein 59 LRRC59 sp|Q96AG4|LRC59_HUMAN Leucine-rich repeat-containing protein 59 OS=Homo sapiens GN=LRRC59 PE=1 SV=19,41Serine/arginine-rich splicing factor 10 SRSF10 tr|Q5JRI1|Q5JRI1_HUMAN Serine/arginine-rich-splicing factor 10 OS=Homo sapiens GN=SRSF10 PE=2 SV=1;sp|O75494-5|SRS10_HUMAN Isoform 5 of Serine/arginine-rich splicing factor 10 OS=Homo sapiens GN=SRSF10;sp|O75494-4|SRS10_HUMAN Isoform 4 of Serine/arginine-r9,39Fragile X mental retardation protein 1 FMR1 sp|Q06787-6|FMR1_HUMAN Isoform 5 of Fragile X mental retardation protein 1 OS=Homo sapiens GN=FMR1;sp|Q06787-4|FMR1_HUMAN Isoform 3 of Fragile X mental retardation protein 1 OS=Homo sapiens GN=FMR1;sp|Q06787-7|FMR1_HUMAN Isoform 7 of Fragile X mental retar9,37Transcription elongation factor B polypeptide 1TCEB1 tr|R4GMY8|R4GMY8_HUMAN Transcription elongation factor B polypeptide 1 OS=Homo sapiens GN=TCEB1 PE=4 SV=1;tr|E5RHG8|E5RHG8_HUMAN Transcription elongation factor B polypeptide 1 (Fragment) OS=Homo sapiens GN=TCEB1 PE=2 SV=1;sp|Q15369-2|ELOC_HUMAN Isoform 2 9,35DnaJ homolog subfamily C member 21 DNAJC21 sp|Q5F1R6|DJC21_HUMAN DnaJ homolog subfamily C member 21 OS=Homo sapiens GN=DNAJC21 PE=1 SV=2;sp|Q5F1R6-3|DJC21_HUMAN Isoform 3 of DnaJ homolog subfamily C member 21 OS=Homo sapiens GN=DNAJC21;sp|Q5F1R6-2|DJC21_HUMAN Isoform 2 of DnaJ homolog subfamily C m9,32N-acetyltransferase 10 NAT10 tr|E7ESU4|E7ESU4_HUMAN N-acetyltransferase 10 OS=Homo sapiens GN=NAT10 PE=2 SV=1;sp|Q9H0A0|NAT10_HUMAN N-acetyltransferase 10 OS=Homo sapiens GN=NAT10 PE=1 SV=29,31SWI/SNF complex subunit SMARCC2 SMARCC2 sp|Q8TAQ2|SMRC2_HUMAN SWI/SNF complex subunit SMARCC2 OS=Homo sapiens GN=SMARCC2 PE=1 SV=1;tr|F8VXC8|F8VXC8_HUMAN SWI/SNF complex subunit SMARCC2 OS=Homo sapiens GN=SMARCC2 PE=2 SV=1;sp|Q8TAQ2-2|SMRC2_HUMAN Isoform 2 of SWI/SNF complex subunit SMARCC2 OS=H9,29Heterogeneous nuclear ribonucleoprotein D0HNRNPD tr|D6RAF8|D6RAF8_HUMAN Heterogeneous nuclear ribonucleoprotein D0 (Fragment) OS=Homo sapiens GN=HNRNPD PE=2 SV=1;sp|Q14103-3|HNRPD_HUMAN Isoform 3 of Heterogeneous nuclear ribonucleoprotein D0 OS=Homo sapiens GN=HNRNPD;sp|Q14103|HNRPD_HUMAN Heterogeneous n9,16PERQ amino acid-rich with GYF domain-containing protein 2GIGYF2 sp|Q6Y7W6-4|PERQ2_HUMAN Isoform 3 of PERQ amino acid-rich with GYF domain-containing protein 2 OS=Homo sapiens GN=GIGYF2;sp|Q6Y7W6-5|PERQ2_HUMAN Isoform 4 of PERQ amino acid-rich with GYF domain-containing protein 2 OS=Homo sapiens GN=GIGYF2;sp|Q6Y7W6|PERQ9,13Peptidyl-prolyl cis-trans isomerase B PPIB sp|P23284|PPIB_HUMAN Peptidyl-prolyl cis-trans isomerase B OS=Homo sapiens GN=PPIB PE=1 SV=29,10Apoptosis-stimulating of p53 protein 2 TP53BP2 sp|Q13625-2|ASPP2_HUMAN Isoform 2 of Apoptosis-stimulating of p53 protein 2 OS=Homo sapiens GN=TP53BP2;sp|Q13625|ASPP2_HUMAN Apoptosis-stimulating of p53 protein 2 OS=Homo sapiens GN=TP53BP2 PE=1 SV=2;sp|Q13625-3|ASPP2_HUMAN Isoform 3 of Apoptosis-stimulat9,08Serine/arginine-rich splicing factor 2 SRSF2 tr|J3QL05|J3QL05_HUMAN Serine/arginine-rich-splicing factor 2 (Fragment) OS=Homo sapiens GN=SRSF2 PE=2 SV=1;tr|J3KP15|J3KP15_HUMAN Serine/arginine-rich-splicing factor 2 (Fragment) OS=Homo sapiens GN=SRSF2 PE=2 SV=1;tr|B4DN89|B4DN89_HUMAN Serine/arginine-r9,05Aspartyl/asparaginyl beta-hydroxylase ASPH sp|Q12797-10|ASPH_HUMAN Isoform 10 of Aspartyl/asparaginyl beta-hydroxylase OS=Homo sapiens GN=ASPH;sp|Q12797|ASPH_HUMAN Aspartyl/asparaginyl beta-hydroxylase OS=Homo sapiens GN=ASPH PE=1 SV=3;tr|E5RHK2|E5RHK2_HUMAN Aspartyl/asparaginyl beta-hydroxylase (F9,03Importin subunit alpha-1 KPNA2 sp|P52292|IMA1_HUMAN Importin subunit alpha-1 OS=Homo sapiens GN=KPNA2 PE=1 SV=1;tr|J3QLL0|J3QLL0_HUMAN Importin subunit alpha-1 (Fragment) OS=Homo sapiens GN=KPNA2 PE=2 SV=1;tr|J3KS65|J3KS65_HUMAN Importin subunit alpha-1 (Fragment) OS=Homo sapiens GN=KPN8,96pre-mRNA 3 end processing protein WDR33 WDR33 sp|Q9C0J8|WDR33_HUMAN pre-mRNA 3 end processing protein WDR33 OS=Homo sapiens GN=WDR33 PE=1 SV=28,94Negative elongation factor E NELFE sp|P18615|NELFE_HUMAN Negative elongation factor E OS=Homo sapiens GN=NELFE PE=1 SV=3;tr|B4DYX9|B4DYX9_HUMAN Negative elongation factor E OS=Homo sapiens GN=NELFE PE=2 SV=1;tr|A2ABK2|A2ABK2_HUMAN Negative elongation factor E (Fragment) OS=Homo sapiens GN=N8,90Constitutive coactivator of PPAR-gamma-like protein 1FAM120A sp|Q9NZB2-4|F120A_HUMAN Isoform D of Constitutive coactivator of PPAR-gamma-like protein 1 OS=Homo sapiens GN=FAM120A;sp|Q9NZB2|F120A_HUMAN Constitutive coactivator of PPAR-gamma-like protein 1 OS=Homo sapiens GN=FAM120A PE=1 SV=2;sp|Q9NZB2-6|F120A_HUMAN I8,8160S ribosomal protein L26-like 1 RPL26L1 sp|Q9UNX3|RL26L_HUMAN 60S ribosomal protein L26-like 1 OS=Homo sapiens GN=RPL26L1 PE=1 SV=1;tr|E5RIT6|E5RIT6_HUMAN 60S ribosomal protein L26-like 1 (Fragment) OS=Homo sapiens GN=RPL26L1 PE=2 SV=18,78Superkiller viralicidic activity 2-like 2 SKIV2L2 sp|P42285|SK2L2_HUMAN Superkiller viralicidic activity 2-like 2 OS=Homo sapiens GN=SKIV2L2 PE=1 SV=3;tr|F5H7E2|F5H7E2_HUMAN Superkiller viralicidic activity 2-like 2 OS=Homo sapiens GN=SKIV2L2 PE=2 SV=18,76BRCA1-A complex subunit BRE BRE tr|F8W733|F8W733_HUMAN BRCA1-A complex subunit BRE (Fragment) OS=Homo sapiens GN=BRE PE=2 SV=1;sp|Q9NXR7-4|BRE_HUMAN Isoform 4 of BRCA1-A complex subunit BRE OS=Homo sapiens GN=BRE;sp|Q9NXR7-3|BRE_HUMAN Isoform 3 of BRCA1-A complex subunit BRE OS=Homo sapi8,75Replication factor C subunit 1 RFC1 sp|P35251-2|RFC1_HUMAN Isoform 2 of Replication factor C subunit 1 OS=Homo sapiens GN=RFC1;sp|P35251|RFC1_HUMAN Replication factor C subunit 1 OS=Homo sapiens GN=RFC1 PE=1 SV=48,74Elongation factor 1-alpha 2 EEF1A2 sp|Q05639|EF1A2_HUMAN Elongation factor 1-alpha 2 OS=Homo sapiens GN=EEF1A2 PE=1 SV=18,73Calcium homeostasis endoplasmic reticulum proteinCHERP tr|J3QK89|J3QK89_HUMAN Calcium homeostasis endoplasmic reticulum protein OS=Homo sapiens GN=CHERP PE=2 SV=1;sp|Q8IWX8|CHERP_HUMAN Calcium homeostasis endoplasmic reticulum protein OS=Homo sapiens GN=CHERP PE=1 SV=38,7228S ribosomal protein S29, mitochondrial DAP3 tr|V9GZ03|V9GZ03_HUMAN 28S ribosomal protein S29, mitochondrial (Fragment) OS=Homo sapiens GN=DAP3 PE=4 SV=1;tr|V9GYJ9|V9GYJ9_HUMAN 28S ribosomal protein S29, mitochondrial (Fragment) OS=Homo sapiens GN=DAP3 PE=4 SV=1;tr|V9GYL9|V9GYL9_HUMAN 28S ribosomal p8,72Testis-specific Y-encoded-like protein 5 TSPYL5 sp|Q86VY4|TSYL5_HUMAN Testis-specific Y-encoded-like protein 5 OS=Homo sapiens GN=TSPYL5 PE=1 SV=28,68Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferaseNOP2 sp|P46087-2|NOP2_HUMAN Isoform 2 of Putative ribosomal RNA methyltransferase NOP2 OS=Homo sapiens GN=NOP2;sp|P46087|NOP2_HUMAN Putative ribosomal RNA methyltransferase NOP2 OS=Homo sapiens GN=NOP2 PE=1 SV=2;sp|P46087-4|NOP2_HUMAN Isoform 4 of Putative ribo8,68Programmed cell death protein 6 PDCD6 sp|O75340-2|PDCD6_HUMAN Isoform 2 of Programmed cell death protein 6 OS=Homo sapiens GN=PDCD6;sp|O75340|PDCD6_HUMAN Programmed cell death protein 6 OS=Homo sapiens GN=PDCD6 PE=1 SV=18,60Aspartate--tRNA ligase, cytoplasmic DARS sp|P14868|SYDC_HUMAN Aspartate--tRNA ligase, cytoplasmic OS=Homo sapiens GN=DARS PE=1 SV=2;tr|Q68CR9|Q68CR9_HUMAN Aspartate--tRNA ligase, cytoplasmic OS=Homo sapiens GN=DKFZp781B11202 PE=2 SV=18,60Delta(24)-sterol reductase DHCR24 tr|H7C4B7|H7C4B7_HUMAN Delta(24)-sterol reductase (Fragment) OS=Homo sapiens GN=DHCR24 PE=4 SV=1;tr|F5H0H1|F5H0H1_HUMAN Delta(24)-sterol reductase OS=Homo sapiens GN=DHCR24 PE=2 SV=1;tr|B7Z817|B7Z817_HUMAN Delta(24)-sterol reductase OS=Homo sapiens GN=DHCR8,59

Page 35: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Protein LSM14 homolog B LSM14B tr|Q5TBP9|Q5TBP9_HUMAN Protein LSM14 homolog B (Fragment) OS=Homo sapiens GN=LSM14B PE=2 SV=1;sp|Q9BX40|LS14B_HUMAN Protein LSM14 homolog B OS=Homo sapiens GN=LSM14B PE=1 SV=1;tr|Q5TBQ0|Q5TBQ0_HUMAN Protein LSM14 homolog B (Fragment) OS=Homo sapiens GN=LSM8,58Histone H2B type 2-E;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 3-BHIST2H2BE;HIST1H2BB;HIST1H2BO;HIST1H2BJ;HIST3H2BBsp|Q16778|H2B2E_HUMAN Histone H2B type 2-E OS=Homo sapiens GN=HIST2H2BE PE=1 SV=3;sp|P33778|H2B1B_HUMAN Histone H2B type 1-B OS=Homo sapiens GN=HIST1H2BB PE=1 SV=2;sp|P23527|H2B1O_HUMAN Histone H2B type 1-O OS=Homo sapiens GN=HIST1H2BO PE=1 SV=3;sp|P06899|8,51X-ray repair cross-complementing protein 5 XRCC5 sp|P13010|XRCC5_HUMAN X-ray repair cross-complementing protein 5 OS=Homo sapiens GN=XRCC5 PE=1 SV=38,48Tubby-related protein 4 TULP4 sp|Q9NRJ4|TULP4_HUMAN Tubby-related protein 4 OS=Homo sapiens GN=TULP4 PE=2 SV=28,47U3 small nucleolar RNA-associated protein 18 homologUTP18 sp|Q9Y5J1|UTP18_HUMAN U3 small nucleolar RNA-associated protein 18 homolog OS=Homo sapiens GN=UTP18 PE=1 SV=38,45SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2SMARCD2 tr|J3KMX2|J3KMX2_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 OS=Homo sapiens GN=SMARCD2 PE=2 SV=1;sp|Q92925-3|SMRD2_HUMAN Isoform 3 of SWI/SNF-related matrix-associated actin-dependent regulator of ch8,43Protein regulator of cytokinesis 1 PRC1 tr|F8W9B5|F8W9B5_HUMAN Protein regulator of cytokinesis 1 OS=Homo sapiens GN=PRC1 PE=2 SV=1;sp|O43663-3|PRC1_HUMAN Isoform 3 of Protein regulator of cytokinesis 1 OS=Homo sapiens GN=PRC1;sp|O43663-2|PRC1_HUMAN Isoform 2 of Protein regulator of cytokinesis 8,39Cleavage and polyadenylation specificity factor subunit 1CPSF1 sp|Q10570|CPSF1_HUMAN Cleavage and polyadenylation specificity factor subunit 1 OS=Homo sapiens GN=CPSF1 PE=1 SV=28,39U4/U6.U5 tri-snRNP-associated protein 1 SART1 sp|O43290|SNUT1_HUMAN U4/U6.U5 tri-snRNP-associated protein 1 OS=Homo sapiens GN=SART1 PE=1 SV=18,38Heterogeneous nuclear ribonucleoprotein L HNRNPL sp|P14866|HNRPL_HUMAN Heterogeneous nuclear ribonucleoprotein L OS=Homo sapiens GN=HNRNPL PE=1 SV=2;tr|M0QXS5|M0QXS5_HUMAN Heterogeneous nuclear ribonucleoprotein L (Fragment) OS=Homo sapiens GN=HNRNPL PE=4 SV=1;sp|P14866-2|HNRPL_HUMAN Isoform 2 of Heterog8,36Histone H2A;Histone H2A.V;Histone H2A.Z H2AFV;H2AFZ tr|C9J0D1|C9J0D1_HUMAN Histone H2A OS=Homo sapiens GN=H2AFV PE=2 SV=1;sp|Q71UI9-2|H2AV_HUMAN Isoform 2 of Histone H2A.V OS=Homo sapiens GN=H2AFV;sp|Q71UI9|H2AV_HUMAN Histone H2A.V OS=Homo sapiens GN=H2AFV PE=1 SV=3;sp|P0C0S5|H2AZ_HUMAN Histone H2A.Z OS=Hom8,35Arginine--tRNA ligase, cytoplasmic RARS sp|P54136|SYRC_HUMAN Arginine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=RARS PE=1 SV=2;sp|P54136-2|SYRC_HUMAN Isoform Monomeric of Arginine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=RARS;tr|F5H3T8|F5H3T8_HUMAN Arginine--tRNA ligase, cytoplasmic OS=Ho8,33YTH domain-containing family protein 3 YTHDF3 tr|R4GN55|R4GN55_HUMAN YTH domain-containing family protein 3 OS=Homo sapiens GN=YTHDF3 PE=4 SV=1;sp|Q7Z739|YTHD3_HUMAN YTH domain-containing family protein 3 OS=Homo sapiens GN=YTHDF3 PE=1 SV=18,17Probable ATP-dependent RNA helicase YTHDC2YTHDC2 sp|Q9H6S0|YTDC2_HUMAN Probable ATP-dependent RNA helicase YTHDC2 OS=Homo sapiens GN=YTHDC2 PE=1 SV=2;tr|D6RA70|D6RA70_HUMAN Probable ATP-dependent RNA helicase YTHDC2 OS=Homo sapiens GN=YTHDC2 PE=2 SV=18,09Protein lin-7 homolog C LIN7C sp|Q9NUP9|LIN7C_HUMAN Protein lin-7 homolog C OS=Homo sapiens GN=LIN7C PE=1 SV=1;tr|G3V1D4|G3V1D4_HUMAN Lin-7 homolog C (C. elegans), isoform CRA_b OS=Homo sapiens GN=LIN7C PE=2 SV=17,89SRSF protein kinase 1 SRPK1 tr|Q5R363|Q5R363_HUMAN SRSF protein kinase 1 OS=Homo sapiens GN=SRPK1 PE=2 SV=1;tr|H3BLV9|H3BLV9_HUMAN SRSF protein kinase 1 (Fragment) OS=Homo sapiens GN=SRPK1 PE=2 SV=1;tr|B4DS61|B4DS61_HUMAN SFRS protein kinase 1, isoform CRA_f OS=Homo sapiens GN=SRPK1 7,85Regulator of nonsense transcripts 1 UPF1 sp|Q92900-2|RENT1_HUMAN Isoform 2 of Regulator of nonsense transcripts 1 OS=Homo sapiens GN=UPF1;sp|Q92900|RENT1_HUMAN Regulator of nonsense transcripts 1 OS=Homo sapiens GN=UPF1 PE=1 SV=27,78Protein LYRIC MTDH sp|Q86UE4|LYRIC_HUMAN Protein LYRIC OS=Homo sapiens GN=MTDH PE=1 SV=2;tr|E5RJU9|E5RJU9_HUMAN Protein LYRIC OS=Homo sapiens GN=MTDH PE=2 SV=17,76Splicing factor 3B subunit 5 SF3B5 sp|Q9BWJ5|SF3B5_HUMAN Splicing factor 3B subunit 5 OS=Homo sapiens GN=SF3B5 PE=1 SV=17,76Importin subunit alpha-4 KPNA3 sp|O00505|IMA4_HUMAN Importin subunit alpha-4 OS=Homo sapiens GN=KPNA3 PE=1 SV=27,72Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2HNRNPH1;HNRNPH2tr|G8JLB6|G8JLB6_HUMAN Heterogeneous nuclear ribonucleoprotein H OS=Homo sapiens GN=HNRNPH1 PE=2 SV=1;sp|P31943|HNRH1_HUMAN Heterogeneous nuclear ribonucleoprotein H OS=Homo sapiens GN=HNRNPH1 PE=1 SV=4;tr|E9PCY7|E9PCY7_HUMAN Heterogeneous nuclear ribonucl7,66Cyclin-T1 CCNT1 sp|O60563|CCNT1_HUMAN Cyclin-T1 OS=Homo sapiens GN=CCNT1 PE=1 SV=17,63Transcription initiation factor IIB GTF2B sp|Q00403|TF2B_HUMAN Transcription initiation factor IIB OS=Homo sapiens GN=GTF2B PE=1 SV=17,60WD repeat-containing protein 89 WDR89 tr|G3V4B8|G3V4B8_HUMAN WD repeat-containing protein 89 (Fragment) OS=Homo sapiens GN=WDR89 PE=2 SV=1;sp|Q96FK6|WDR89_HUMAN WD repeat-containing protein 89 OS=Homo sapiens GN=WDR89 PE=1 SV=17,60Heterogeneous nuclear ribonucleoprotein H3HNRNPH3 tr|B4DHY1|B4DHY1_HUMAN Heterogeneous nuclear ribonucleoprotein H3 OS=Homo sapiens GN=HNRNPH3 PE=2 SV=1;sp|P31942-4|HNRH3_HUMAN Isoform 4 of Heterogeneous nuclear ribonucleoprotein H3 OS=Homo sapiens GN=HNRNPH3;sp|P31942-3|HNRH3_HUMAN Isoform 3 of Heterogen7,60SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminalSRPK2 sp|P78362|SRPK2_HUMAN SRSF protein kinase 2 OS=Homo sapiens GN=SRPK2 PE=1 SV=3;sp|P78362-2|SRPK2_HUMAN Isoform 2 of SRSF protein kinase 2 OS=Homo sapiens GN=SRPK27,543-5 exoribonuclease 1 ERI1 sp|Q8IV48|ERI1_HUMAN 3-5 exoribonuclease 1 OS=Homo sapiens GN=ERI1 PE=1 SV=3;tr|E5RIV7|E5RIV7_HUMAN 3-5 exoribonuclease 1 OS=Homo sapiens GN=ERI1 PE=2 SV=17,48Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A.J;Histone H2A type 2-C;Histone H2A type 1-C;Histone H2A type 2-A;Histone H2A type 1;Histone H2A type 1-A;Histone H2A type 2-B;Histone H2A type 3;Histone H2A type 1-D;Histone H2A type 1-B/E;Histone H2AX;Histone H2AHIST1H2AJ;HIST1H2AH;H2AFJ;HIST2H2AC;HIST1H2AC;HIST2H2AA3;HIST1H2AG;HIST1H2AA;HIST2H2AB;HIST3H2A;HIST1H2AD;HIST1H2AB;H2AFXsp|Q99878|H2A1J_HUMAN Histone H2A type 1-J OS=Homo sapiens GN=HIST1H2AJ PE=1 SV=3;sp|Q96KK5|H2A1H_HUMAN Histone H2A type 1-H OS=Homo sapiens GN=HIST1H2AH PE=1 SV=3;sp|Q9BTM1|H2AJ_HUMAN Histone H2A.J OS=Homo sapiens GN=H2AFJ PE=1 SV=1;sp|Q16777|H2A2C_HUMAN 7,45ATP-binding cassette sub-family F member 2 ABCF2 sp|Q9UG63|ABCF2_HUMAN ATP-binding cassette sub-family F member 2 OS=Homo sapiens GN=ABCF2 PE=1 SV=2;tr|Q75MJ1|Q75MJ1_HUMAN ATP-binding cassette sub-family F member 2 OS=Homo sapiens GN=ABCF2 PE=2 SV=17,45Glutamine--tRNA ligase QARS sp|P47897|SYQ_HUMAN Glutamine--tRNA ligase OS=Homo sapiens GN=QARS PE=1 SV=1;tr|B4DWJ2|B4DWJ2_HUMAN Glutamine--tRNA ligase OS=Homo sapiens GN=QARS PE=2 SV=1;tr|H7C0R3|H7C0R3_HUMAN Glutamine--tRNA ligase (Fragment) OS=Homo sapiens GN=QARS PE=2 SV=17,40Dynein light chain 2, cytoplasmic DYNLL2 sp|Q96FJ2|DYL2_HUMAN Dynein light chain 2, cytoplasmic OS=Homo sapiens GN=DYNLL2 PE=1 SV=17,40KH domain-containing, RNA-binding, signal transduction-associated protein 1KHDRBS1 sp|Q07666-3|KHDR1_HUMAN Isoform 3 of KH domain-containing, RNA-binding, signal transduction-associated protein 1 OS=Homo sapiens GN=KHDRBS1;sp|Q07666-2|KHDR1_HUMAN Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1 OS=7,35Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase PP1-alpha catalytic subunitPPP1CA tr|E9PMD7|E9PMD7_HUMAN Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (Fragment) OS=Homo sapiens GN=PPP1CA PE=2 SV=1;sp|P62136|PP1A_HUMAN Serine/threonine-protein phosphatase PP1-alpha catalytic subunit OS=Homo sapiens GN=PPP1CA PE=1 SV=17,35Putative tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferaseFTSJ1 sp|Q9UET6-2|TRM7_HUMAN Isoform 2 of Putative tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase OS=Homo sapiens GN=FTSJ1;sp|Q9UET6|TRM7_HUMAN Putative tRNA (cytidine(32)/guanosine(34)-2-O)-methyltransferase OS=Homo sapiens GN=FTSJ1 PE=1 SV=2;tr|B7Z47,34Histone H2B;Histone H2B type 1-L;Histone H2B type 1-M;Histone H2B type 1-N;Histone H2B type 1-H;Histone H2B type 2-F;Histone H2B type 1-C/E/F/G/I;Histone H2B type 1-D;Histone H2B type F-S;Histone H2B type 1-K;Histone H2B type 1-AHIST1H2BN;HIST1H2BL;HIST1H2BM;HIST1H2BH;HIST2H2BF;HIST1H2BC;HIST1H2BD;H2BFS;HIST1H2BK;HIST1H2BAtr|U3KQK0|U3KQK0_HUMAN Histone H2B OS=Homo sapiens GN=HIST1H2BN PE=3 SV=1;tr|B4DR52|B4DR52_HUMAN Histone H2B OS=Homo sapiens GN=HIST2H2BF PE=2 SV=1;sp|Q99880|H2B1L_HUMAN Histone H2B type 1-L OS=Homo sapiens GN=HIST1H2BL PE=1 SV=3;sp|Q99879|H2B1M_HUMAN Hist7,34U1 small nuclear ribonucleoprotein 70 kDa SNRNP70 sp|P08621-2|RU17_HUMAN Isoform 2 of U1 small nuclear ribonucleoprotein 70 kDa OS=Homo sapiens GN=SNRNP70;sp|P08621|RU17_HUMAN U1 small nuclear ribonucleoprotein 70 kDa OS=Homo sapiens GN=SNRNP70 PE=1 SV=2;sp|P08621-3|RU17_HUMAN Isoform 3 of U1 small nuclea7,33Tight junction protein ZO-1 TJP1 tr|G5E9E7|G5E9E7_HUMAN Tight junction protein 1 (Zona occludens 1), isoform CRA_e OS=Homo sapiens GN=TJP1 PE=2 SV=1;tr|G3V1L9|G3V1L9_HUMAN Tight junction protein 1 (Zona occludens 1), isoform CRA_a OS=Homo sapiens GN=TJP1 PE=2 SV=1;sp|Q07157-2|ZO1_HUMAN Is7,27ATP-dependent RNA helicase DDX18 DDX18 sp|Q9NVP1|DDX18_HUMAN ATP-dependent RNA helicase DDX18 OS=Homo sapiens GN=DDX18 PE=1 SV=27,20Replication factor C subunit 4 RFC4 sp|P35249|RFC4_HUMAN Replication factor C subunit 4 OS=Homo sapiens GN=RFC4 PE=1 SV=2;tr|C9J8M3|C9J8M3_HUMAN Replication factor C subunit 4 (Fragment) OS=Homo sapiens GN=RFC4 PE=2 SV=1;tr|C9JZI1|C9JZI1_HUMAN Replication factor C subunit 4 OS=Homo sapiens G7,18Serine beta-lactamase-like protein LACTB, mitochondrialLACTB sp|P83111-2|LACTB_HUMAN Isoform 2 of Serine beta-lactamase-like protein LACTB, mitochondrial OS=Homo sapiens GN=LACTB;sp|P83111|LACTB_HUMAN Serine beta-lactamase-like protein LACTB, mitochondrial OS=Homo sapiens GN=LACTB PE=1 SV=2;tr|H0YNN5|H0YNN5_HUMAN Se7,15pre-rRNA processing protein FTSJ3 FTSJ3 sp|Q8IY81|SPB1_HUMAN pre-rRNA processing protein FTSJ3 OS=Homo sapiens GN=FTSJ3 PE=1 SV=27,1460S ribosomal protein L36a-like RPL36AL sp|Q969Q0|RL36L_HUMAN 60S ribosomal protein L36a-like OS=Homo sapiens GN=RPL36AL PE=1 SV=37,10Histone-binding protein RBBP4;Histone-binding protein RBBP7RBBP4;RBBP7 sp|Q09028-3|RBBP4_HUMAN Isoform 3 of Histone-binding protein RBBP4 OS=Homo sapiens GN=RBBP4;sp|Q09028|RBBP4_HUMAN Histone-binding protein RBBP4 OS=Homo sapiens GN=RBBP4 PE=1 SV=3;tr|E9PNS2|E9PNS2_HUMAN Histone-binding protein RBBP4 OS=Homo sapiens GN=RBBP47,08Pescadillo homolog PES1 tr|B5MCF9|B5MCF9_HUMAN Pescadillo homolog OS=Homo sapiens GN=PES1 PE=2 SV=1;sp|O00541-2|PESC_HUMAN Isoform 2 of Pescadillo homolog OS=Homo sapiens GN=PES1;sp|O00541|PESC_HUMAN Pescadillo homolog OS=Homo sapiens GN=PES1 PE=1 SV=1;tr|B3KXD6|B3KXD6_HUMAN Pesc7,07ATPase family AAA domain-containing protein 3A;ATPase family AAA domain-containing protein 3BATAD3A;ATAD3B sp|Q9NVI7-2|ATD3A_HUMAN Isoform 2 of ATPase family AAA domain-containing protein 3A OS=Homo sapiens GN=ATAD3A;tr|H0Y2W2|H0Y2W2_HUMAN ATPase family AAA domain-containing protein 3A (Fragment) OS=Homo sapiens GN=ATAD3A PE=4 SV=1;sp|Q9NVI7-3|ATD3A_HUMAN Isofo7,02Ubiquitin carboxyl-terminal hydrolase 15 USP15 sp|Q9Y4E8|UBP15_HUMAN Ubiquitin carboxyl-terminal hydrolase 15 OS=Homo sapiens GN=USP15 PE=1 SV=3;tr|E9PCQ3|E9PCQ3_HUMAN Ubiquitin carboxyl-terminal hydrolase OS=Homo sapiens GN=USP15 PE=2 SV=2;sp|Q9Y4E8-2|UBP15_HUMAN Isoform 2 of Ubiquitin carboxyl-termin7,01Ubiquitin-associated protein 2 UBAP2 tr|E7EWG4|E7EWG4_HUMAN Ubiquitin-associated protein 2 OS=Homo sapiens GN=UBAP2 PE=2 SV=2;sp|Q5T6F2|UBAP2_HUMAN Ubiquitin-associated protein 2 OS=Homo sapiens GN=UBAP2 PE=1 SV=1;tr|A2A305|A2A305_HUMAN Ubiquitin-associated protein 2 (Fragment) OS=Homo sapien6,98rRNA 2-O-methyltransferase fibrillarin FBL sp|P22087|FBRL_HUMAN rRNA 2-O-methyltransferase fibrillarin OS=Homo sapiens GN=FBL PE=1 SV=2;tr|M0R299|M0R299_HUMAN rRNA 2-O-methyltransferase fibrillarin (Fragment) OS=Homo sapiens GN=FBL PE=2 SV=1;tr|M0QXL5|M0QXL5_HUMAN rRNA 2-O-methyltransferase fibr6,98Dehydrogenase/reductase SDR family member 2, mitochondrialDHRS2 sp|Q13268|DHRS2_HUMAN Dehydrogenase/reductase SDR family member 2, mitochondrial OS=Homo sapiens GN=DHRS2 PE=1 SV=4;tr|H0YJG9|H0YJG9_HUMAN Dehydrogenase/reductase SDR family member 2, mitochondrial (Fragment) OS=Homo sapiens GN=DHRS2 PE=2 SV=1;tr|H0YJP4|H06,94Melanoma-associated antigen 4;Melanoma-associated antigen 8MAGEA4;MAGEA8 sp|P43358|MAGA4_HUMAN Melanoma-associated antigen 4 OS=Homo sapiens GN=MAGEA4 PE=1 SV=2;sp|P43361|MAGA8_HUMAN Melanoma-associated antigen 8 OS=Homo sapiens GN=MAGEA8 PE=2 SV=26,89MAGUK p55 subfamily member 5 MPP5 sp|Q8N3R9|MPP5_HUMAN MAGUK p55 subfamily member 5 OS=Homo sapiens GN=MPP5 PE=1 SV=3;sp|Q8N3R9-2|MPP5_HUMAN Isoform 2 of MAGUK p55 subfamily member 5 OS=Homo sapiens GN=MPP56,89Leucine--tRNA ligase, cytoplasmic LARS tr|F5H698|F5H698_HUMAN Leucine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=LARS PE=2 SV=1;tr|B4DER1|B4DER1_HUMAN Leucine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=LARS PE=2 SV=1;tr|B4DJ10|B4DJ10_HUMAN Leucine--tRNA ligase, cytoplasmic OS=Homo sapiens G6,84Transformer-2 protein homolog alpha TRA2A tr|B4DQI6|B4DQI6_HUMAN Transformer-2 protein homolog alpha OS=Homo sapiens GN=TRA2A PE=2 SV=1;tr|B4DUA9|B4DUA9_HUMAN Transformer-2 protein homolog alpha OS=Homo sapiens GN=TRA2A PE=2 SV=1;sp|Q13595|TRA2A_HUMAN Transformer-2 protein homolog alpha OS=Homo sa6,84Vigilin HDLBP sp|Q00341|VIGLN_HUMAN Vigilin OS=Homo sapiens GN=HDLBP PE=1 SV=2;sp|Q00341-2|VIGLN_HUMAN Isoform 2 of Vigilin OS=Homo sapiens GN=HDLBP;tr|H0Y394|H0Y394_HUMAN Vigilin (Fragment) OS=Homo sapiens GN=HDLBP PE=4 SV=16,83Deoxynucleotidyltransferase terminal-interacting protein 1DNTTIP1 sp|Q9H147|TDIF1_HUMAN Deoxynucleotidyltransferase terminal-interacting protein 1 OS=Homo sapiens GN=DNTTIP1 PE=1 SV=2;tr|H7C1M5|H7C1M5_HUMAN Deoxynucleotidyltransferase terminal-interacting protein 1 (Fragment) OS=Homo sapiens GN=DNTTIP1 PE=4 SV=1;tr|H7C1J6,73Nucleolar protein 16 NOP16 sp|Q9Y3C1|NOP16_HUMAN Nucleolar protein 16 OS=Homo sapiens GN=NOP16 PE=1 SV=2;tr|D6RIC3|D6RIC3_HUMAN Nucleolar protein 16 OS=Homo sapiens GN=NOP16 PE=2 SV=1;sp|Q9Y3C1-2|NOP16_HUMAN Isoform 2 of Nucleolar protein 16 OS=Homo sapiens GN=NOP166,73

Page 36: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Isoleucine--tRNA ligase, cytoplasmic IARS sp|P41252|SYIC_HUMAN Isoleucine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=IARS PE=1 SV=2;tr|J3KR24|J3KR24_HUMAN Isoleucine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=IARS PE=2 SV=16,67Nucleolar transcription factor 1 UBTF tr|E9PKP7|E9PKP7_HUMAN Nucleolar transcription factor 1 OS=Homo sapiens GN=UBTF PE=2 SV=1;sp|P17480-2|UBF1_HUMAN Isoform UBF2 of Nucleolar transcription factor 1 OS=Homo sapiens GN=UBTF;sp|P17480|UBF1_HUMAN Nucleolar transcription factor 1 OS=Homo sapiens 6,66Heat shock 70 kDa protein 1A HSPA1A sp|P08107-2|HSP71_HUMAN Isoform 2 of Heat shock 70 kDa protein 1A/1B OS=Homo sapiens GN=HSPA1A;sp|P08107|HSP71_HUMAN Heat shock 70 kDa protein 1A/1B OS=Homo sapiens GN=HSPA1A PE=1 SV=5;tr|E7EP94|E7EP94_HUMAN Heat shock 70 kDa protein 1A/1B OS=Homo sapiens 6,63U2 snRNP-associated SURP motif-containing proteinU2SURP sp|O15042-2|SR140_HUMAN Isoform 2 of U2 snRNP-associated SURP motif-containing protein OS=Homo sapiens GN=U2SURP;sp|O15042|SR140_HUMAN U2 snRNP-associated SURP motif-containing protein OS=Homo sapiens GN=U2SURP PE=1 SV=2;tr|E7ET15|E7ET15_HUMAN U2 snRNP-ass6,58Negative elongation factor A WHSC2;NELFA tr|B3KSP0|B3KSP0_HUMAN Negative elongation factor A OS=Homo sapiens GN=NELFA PE=2 SV=1;tr|H0Y3X6|H0Y3X6_HUMAN Negative elongation factor A (Fragment) OS=Homo sapiens GN=NELFA PE=2 SV=1;sp|Q9H3P2|NELFA_HUMAN Negative elongation factor A OS=Homo sapiens GN=N6,57Putative helicase MOV-10 MOV10 tr|Q5JR04|Q5JR04_HUMAN Mov10, Moloney leukemia virus 10, homolog (Mouse), isoform CRA_a OS=Homo sapiens GN=MOV10 PE=2 SV=1;sp|Q9HCE1|MOV10_HUMAN Putative helicase MOV-10 OS=Homo sapiens GN=MOV10 PE=1 SV=2;sp|Q9HCE1-2|MOV10_HUMAN Isoform 2 of Putative helic6,51Uncharacterized protein CXorf67 CXorf67 sp|Q86X51|CX067_HUMAN Uncharacterized protein CXorf67 OS=Homo sapiens GN=CXorf67 PE=2 SV=16,51Protein HEXIM1 HEXIM1 sp|O94992|HEXI1_HUMAN Protein HEXIM1 OS=Homo sapiens GN=HEXIM1 PE=1 SV=16,45Kinesin-like protein KIFC1 KIFC1 sp|Q9BW19|KIFC1_HUMAN Kinesin-like protein KIFC1 OS=Homo sapiens GN=KIFC1 PE=1 SV=26,44Pre-mRNA-processing-splicing factor 8 PRPF8 sp|Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 OS=Homo sapiens GN=PRPF8 PE=1 SV=26,43Aminoacyl tRNA synthase complex-interacting multifunctional protein 2AIMP2 sp|Q13155|AIMP2_HUMAN Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 OS=Homo sapiens GN=AIMP2 PE=1 SV=2;tr|A8MU58|A8MU58_HUMAN Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 OS=Homo sapiens GN=AIMP2 PE=2 SV=2;t6,43Multiple myeloma tumor-associated protein 2 MMTAG2 sp|Q9BU76-4|MMTA2_HUMAN Isoform 4 of Multiple myeloma tumor-associated protein 2 OS=Homo sapiens GN=MMTAG2;sp|Q9BU76|MMTA2_HUMAN Multiple myeloma tumor-associated protein 2 OS=Homo sapiens GN=MMTAG2 PE=1 SV=1;sp|Q9BU76-3|MMTA2_HUMAN Isoform 3 of Multiple m6,36Nuclear export mediator factor NEMF NEMF sp|O60524-4|NEMF_HUMAN Isoform 4 of Nuclear export mediator factor NEMF OS=Homo sapiens GN=NEMF;sp|O60524-5|NEMF_HUMAN Isoform 5 of Nuclear export mediator factor NEMF OS=Homo sapiens GN=NEMF;sp|O60524-3|NEMF_HUMAN Isoform 3 of Nuclear export mediator fact6,27FACT complex subunit SSRP1 SSRP1 sp|Q08945|SSRP1_HUMAN FACT complex subunit SSRP1 OS=Homo sapiens GN=SSRP1 PE=1 SV=16,25Nucleolar protein 58 NOP58 sp|Q9Y2X3|NOP58_HUMAN Nucleolar protein 58 OS=Homo sapiens GN=NOP58 PE=1 SV=16,23Probable ATP-dependent RNA helicase DDX6DDX6 sp|P26196|DDX6_HUMAN Probable ATP-dependent RNA helicase DDX6 OS=Homo sapiens GN=DDX6 PE=1 SV=26,14Zinc finger CCCH-type antiviral protein 1 ZC3HAV1 sp|Q7Z2W4-2|ZCCHV_HUMAN Isoform 2 of Zinc finger CCCH-type antiviral protein 1 OS=Homo sapiens GN=ZC3HAV1;sp|Q7Z2W4|ZCCHV_HUMAN Zinc finger CCCH-type antiviral protein 1 OS=Homo sapiens GN=ZC3HAV1 PE=1 SV=3;tr|C9J6P4|C9J6P4_HUMAN Zinc finger CCCH-type anti6,13AT-rich interactive domain-containing protein 1BARID1B tr|G3XAA0|G3XAA0_HUMAN AT rich interactive domain 1B (SWI1-like), isoform CRA_a OS=Homo sapiens GN=ARID1B PE=2 SV=1;sp|Q8NFD5|ARI1B_HUMAN AT-rich interactive domain-containing protein 1B OS=Homo sapiens GN=ARID1B PE=1 SV=2;sp|Q8NFD5-2|ARI1B_HUMAN Isoform 26,10Ribosome biogenesis protein BMS1 homologBMS1 sp|Q14692|BMS1_HUMAN Ribosome biogenesis protein BMS1 homolog OS=Homo sapiens GN=BMS1 PE=1 SV=16,08Splicing factor 3B subunit 2 SF3B2 sp|Q13435|SF3B2_HUMAN Splicing factor 3B subunit 2 OS=Homo sapiens GN=SF3B2 PE=1 SV=2;tr|E9PPJ0|E9PPJ0_HUMAN Splicing factor 3B subunit 2 OS=Homo sapiens GN=SF3B2 PE=2 SV=16,06U1 small nuclear ribonucleoprotein C SNRPC sp|P09234|RU1C_HUMAN U1 small nuclear ribonucleoprotein C OS=Homo sapiens GN=SNRPC PE=1 SV=16,06Caveolin-1;Caveolin CAV1 sp|Q03135|CAV1_HUMAN Caveolin-1 OS=Homo sapiens GN=CAV1 PE=1 SV=4;tr|C9JKI3|C9JKI3_HUMAN Caveolin (Fragment) OS=Homo sapiens GN=CAV1 PE=2 SV=1;tr|E9PCT5|E9PCT5_HUMAN Caveolin OS=Homo sapiens GN=CAV1 PE=2 SV=1;sp|Q03135-2|CAV1_HUMAN Isoform Beta of Caveolin6,05RRP12-like protein RRP12 sp|Q5JTH9-2|RRP12_HUMAN Isoform 2 of RRP12-like protein OS=Homo sapiens GN=RRP12;sp|Q5JTH9-3|RRP12_HUMAN Isoform 3 of RRP12-like protein OS=Homo sapiens GN=RRP12;sp|Q5JTH9|RRP12_HUMAN RRP12-like protein OS=Homo sapiens GN=RRP12 PE=1 SV=2;tr|F5H456|F5H456_H5,97Histone deacetylase 1 HDAC1 sp|Q13547|HDAC1_HUMAN Histone deacetylase 1 OS=Homo sapiens GN=HDAC1 PE=1 SV=1;tr|Q5TEE2|Q5TEE2_HUMAN Histone deacetylase 1 (Fragment) OS=Homo sapiens GN=HDAC1 PE=2 SV=1;tr|F5GXM1|F5GXM1_HUMAN Histone deacetylase 1 OS=Homo sapiens GN=HDAC1 PE=2 SV=15,91Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligaseEPRS sp|P07814|SYEP_HUMAN Bifunctional glutamate/proline--tRNA ligase OS=Homo sapiens GN=EPRS PE=1 SV=55,88Histone lysine demethylase PHF8 PHF8 tr|H0Y3N9|H0Y3N9_HUMAN Histone lysine demethylase PHF8 (Fragment) OS=Homo sapiens GN=PHF8 PE=4 SV=1;sp|Q9UPP1-2|PHF8_HUMAN Isoform 2 of Histone lysine demethylase PHF8 OS=Homo sapiens GN=PHF8;sp|Q9UPP1|PHF8_HUMAN Histone lysine demethylase PHF8 OS=Homo sap5,80Replication factor C subunit 2 RFC2 tr|H7C5S7|H7C5S7_HUMAN Replication factor C subunit 2 (Fragment) OS=Homo sapiens GN=RFC2 PE=2 SV=1;tr|H7C5P1|H7C5P1_HUMAN Replication factor C subunit 2 (Fragment) OS=Homo sapiens GN=RFC2 PE=4 SV=1;tr|H7C5Q7|H7C5Q7_HUMAN Replication factor C subunit 2 (Fra5,80Exosome component 10 EXOSC10 sp|Q01780|EXOSX_HUMAN Exosome component 10 OS=Homo sapiens GN=EXOSC10 PE=1 SV=2;sp|Q01780-2|EXOSX_HUMAN Isoform 2 of Exosome component 10 OS=Homo sapiens GN=EXOSC10;tr|B4DKG8|B4DKG8_HUMAN Exosome component 10 OS=Homo sapiens GN=EXOSC10 PE=2 SV=15,74Cell growth-regulating nucleolar protein LYAR sp|Q9NX58|LYAR_HUMAN Cell growth-regulating nucleolar protein OS=Homo sapiens GN=LYAR PE=1 SV=25,73Aminoacyl tRNA synthase complex-interacting multifunctional protein 1;Endothelial monocyte-activating polypeptide 2AIMP1 sp|Q12904|AIMP1_HUMAN Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 OS=Homo sapiens GN=AIMP1 PE=1 SV=2;sp|Q12904-2|AIMP1_HUMAN Isoform 2 of Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 OS=Homo sapiens GN=AIM5,71Segment polarity protein dishevelled homolog DVL-2DVL2 sp|O14641|DVL2_HUMAN Segment polarity protein dishevelled homolog DVL-2 OS=Homo sapiens GN=DVL2 PE=1 SV=1;tr|I3L2N2|I3L2N2_HUMAN Segment polarity protein dishevelled homolog DVL-2 OS=Homo sapiens GN=DVL2 PE=2 SV=1;tr|I3L2W9|I3L2W9_HUMAN Segment polarity pr5,58Transcription intermediary factor 1-beta TRIM28 sp|Q13263|TIF1B_HUMAN Transcription intermediary factor 1-beta OS=Homo sapiens GN=TRIM28 PE=1 SV=5;tr|M0R0K9|M0R0K9_HUMAN Transcription intermediary factor 1-beta (Fragment) OS=Homo sapiens GN=TRIM28 PE=2 SV=1;sp|Q13263-2|TIF1B_HUMAN Isoform 2 of Transcrip5,55DnaJ homolog subfamily C member 13 DNAJC13 sp|O75165|DJC13_HUMAN DnaJ homolog subfamily C member 13 OS=Homo sapiens GN=DNAJC13 PE=1 SV=55,53Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a;Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40;Polyubiquitin-B;Ubiquitin;Polyubiquitin-C;UbiquitinRPS27A;UBB;UBC;UBA52sp|P62979|RS27A_HUMAN Ubiquitin-40S ribosomal protein S27a OS=Homo sapiens GN=RPS27A PE=1 SV=2;tr|J3QS39|J3QS39_HUMAN Ubiquitin (Fragment) OS=Homo sapiens GN=UBB PE=2 SV=1;tr|J3QTR3|J3QTR3_HUMAN Ubiquitin (Fragment) OS=Homo sapiens GN=RPS27A PE=1 SV=1;tr|F5,52Ribosome production factor 2 homolog RPF2 sp|Q9H7B2|RPF2_HUMAN Ribosome production factor 2 homolog OS=Homo sapiens GN=RPF2 PE=1 SV=2;tr|Q5VXN0|Q5VXN0_HUMAN Ribosome production factor 2 homolog (Fragment) OS=Homo sapiens GN=RPF2 PE=2 SV=15,51RNA-binding protein 28 RBM28 sp|Q9NW13|RBM28_HUMAN RNA-binding protein 28 OS=Homo sapiens GN=RBM28 PE=1 SV=3;tr|C9JE21|C9JE21_HUMAN RNA-binding protein 28 (Fragment) OS=Homo sapiens GN=RBM28 PE=2 SV=1;sp|Q9NW13-2|RBM28_HUMAN Isoform 2 of RNA-binding protein 28 OS=Homo sapiens GN=RBM285,29WD repeat-containing protein 6 WDR6 tr|E9PDU5|E9PDU5_HUMAN WD repeat-containing protein 6 OS=Homo sapiens GN=WDR6 PE=2 SV=1;sp|Q9NNW5|WDR6_HUMAN WD repeat-containing protein 6 OS=Homo sapiens GN=WDR6 PE=1 SV=1;tr|E9PBK6|E9PBK6_HUMAN WD repeat-containing protein 6 OS=Homo sapiens GN=WDR6 PE=25,27Ataxin-2-like protein ATXN2L tr|H3BUF6|H3BUF6_HUMAN Ataxin-2-like protein OS=Homo sapiens GN=ATXN2L PE=2 SV=1;sp|Q8WWM7-6|ATX2L_HUMAN Isoform 6 of Ataxin-2-like protein OS=Homo sapiens GN=ATXN2L;sp|Q8WWM7-8|ATX2L_HUMAN Isoform 8 of Ataxin-2-like protein OS=Homo sapiens GN=ATXN2L;sp|Q85,25Chromatin target of PRMT1 protein CHTOP sp|Q9Y3Y2-4|CHTOP_HUMAN Isoform 3 of Chromatin target of PRMT1 protein OS=Homo sapiens GN=CHTOP;sp|Q9Y3Y2|CHTOP_HUMAN Chromatin target of PRMT1 protein OS=Homo sapiens GN=CHTOP PE=1 SV=2;sp|Q9Y3Y2-3|CHTOP_HUMAN Isoform 2 of Chromatin target of PRMT1 protei5,23Matrin-3 MATR3 tr|D6REM6|D6REM6_HUMAN Matrin-3 OS=Homo sapiens GN=MATR3 PE=2 SV=1;tr|A8MXP9|A8MXP9_HUMAN Matrin-3 OS=Homo sapiens GN=MATR3 PE=2 SV=1;sp|P43243|MATR3_HUMAN Matrin-3 OS=Homo sapiens GN=MATR3 PE=1 SV=2;tr|D6R991|D6R991_HUMAN Matrin-3 (Fragment) OS=Homo sapie5,23Activating signal cointegrator 1 complex subunit 3ASCC3 sp|Q8N3C0|ASCC3_HUMAN Activating signal cointegrator 1 complex subunit 3 OS=Homo sapiens GN=ASCC3 PE=1 SV=35,21Nucleolar GTP-binding protein 2 GNL2 sp|Q13823|NOG2_HUMAN Nucleolar GTP-binding protein 2 OS=Homo sapiens GN=GNL2 PE=1 SV=15,20G patch domain-containing protein 4 GPATCH4 tr|E9PAV9|E9PAV9_HUMAN G patch domain-containing protein 4 OS=Homo sapiens GN=GPATCH4 PE=2 SV=1;sp|Q5T3I0|GPTC4_HUMAN G patch domain-containing protein 4 OS=Homo sapiens GN=GPATCH4 PE=1 SV=2;sp|Q5T3I0-3|GPTC4_HUMAN Isoform 3 of G patch domain-containing pr5,16Ribonuclease 3 DROSHA sp|Q9NRR4|RNC_HUMAN Ribonuclease 3 OS=Homo sapiens GN=DROSHA PE=1 SV=2;sp|Q9NRR4-3|RNC_HUMAN Isoform 3 of Ribonuclease 3 OS=Homo sapiens GN=DROSHA;sp|Q9NRR4-2|RNC_HUMAN Isoform 2 of Ribonuclease 3 OS=Homo sapiens GN=DROSHA;sp|Q9NRR4-4|RNC_HUMAN Isoform 4 o5,16Heterogeneous nuclear ribonucleoprotein K HNRNPK tr|Q5T6W5|Q5T6W5_HUMAN Heterogeneous nuclear ribonucleoprotein K OS=Homo sapiens GN=HNRNPK PE=4 SV=1;sp|P61978-3|HNRPK_HUMAN Isoform 3 of Heterogeneous nuclear ribonucleoprotein K OS=Homo sapiens GN=HNRNPK;sp|P61978|HNRPK_HUMAN Heterogeneous nuclear ribonu5,15Squamous cell carcinoma antigen recognized by T-cells 3SART3 tr|F8VV04|F8VV04_HUMAN Squamous cell carcinoma antigen recognized by T-cells 3 (Fragment) OS=Homo sapiens GN=SART3 PE=2 SV=1;tr|B7ZKM0|B7ZKM0_HUMAN SART3 protein OS=Homo sapiens GN=SART3 PE=2 SV=1;sp|Q15020|SART3_HUMAN Squamous cell carcinoma antigen recog5,14CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;DihydroorotaseCAD tr|F8VPD4|F8VPD4_HUMAN CAD protein OS=Homo sapiens GN=CAD PE=2 SV=1;sp|P27708|PYR1_HUMAN CAD protein OS=Homo sapiens GN=CAD PE=1 SV=35,14Putative eukaryotic translation initiation factor 2 subunit 3-like protein;Eukaryotic translation initiation factor 2 subunit 3EIF2S3L;EIF2S3 tr|F8W810|F8W810_HUMAN Uncharacterized protein OS=Homo sapiens PE=2 SV=1;sp|Q2VIR3-2|IF2GL_HUMAN Isoform 2 of Putative eukaryotic translation initiation factor 2 subunit 3-like protein OS=Homo sapiens GN=EIF2S3L;sp|Q2VIR3|IF2GL_HUMAN Putative eukaryotic tr5,13Histone H4 HIST1H4A sp|P62805|H4_HUMAN Histone H4 OS=Homo sapiens GN=HIST1H4A PE=1 SV=25,11Histone deacetylase 2 HDAC2 tr|J3KPW7|J3KPW7_HUMAN Histone deacetylase 2 OS=Homo sapiens GN=HDAC2 PE=2 SV=1;tr|B3KRS5|B3KRS5_HUMAN Histone deacetylase OS=Homo sapiens GN=HDAC2 PE=2 SV=1;sp|Q92769|HDAC2_HUMAN Histone deacetylase 2 OS=Homo sapiens GN=HDAC2 PE=1 SV=2;tr|H3BM24|H3BM24_HU5,11Serine/threonine-protein phosphatase PP1-beta catalytic subunit;Serine/threonine-protein phosphatasePPP1CB sp|P62140|PP1B_HUMAN Serine/threonine-protein phosphatase PP1-beta catalytic subunit OS=Homo sapiens GN=PPP1CB PE=1 SV=3;tr|C9J9S3|C9J9S3_HUMAN Serine/threonine-protein phosphatase PP1-beta catalytic subunit (Fragment) OS=Homo sapiens GN=PPP1CB PE=2 SV=1;t5,11FACT complex subunit SPT16 SUPT16H sp|Q9Y5B9|SP16H_HUMAN FACT complex subunit SPT16 OS=Homo sapiens GN=SUPT16H PE=1 SV=15,06Probable global transcription activator SNF2L1;SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5SMARCA1;SMARCA5sp|P28370-2|SMCA1_HUMAN Isoform 2 of Probable global transcription activator SNF2L1 OS=Homo sapiens GN=SMARCA1;sp|O60264|SMCA5_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 OS=Homo sapiens GN=SMARCA5 PE5,05V-type proton ATPase 116 kDa subunit a isoform 3;V-type proton ATPase subunit aTCIRG1 sp|Q13488-2|VPP3_HUMAN Isoform Short of V-type proton ATPase 116 kDa subunit a isoform 3 OS=Homo sapiens GN=TCIRG1;sp|Q13488|VPP3_HUMAN V-type proton ATPase 116 kDa subunit a isoform 3 OS=Homo sapiens GN=TCIRG1 PE=1 SV=3;tr|H0YEL3|H0YEL3_HUMAN V-type proto5,02DNA-dependent protein kinase catalytic subunitPRKDC tr|E7EUY0|E7EUY0_HUMAN DNA-dependent protein kinase catalytic subunit OS=Homo sapiens GN=PRKDC PE=2 SV=1;sp|P78527-2|PRKDC_HUMAN Isoform 2 of DNA-dependent protein kinase catalytic subunit OS=Homo sapiens GN=PRKDC;sp|P78527|PRKDC_HUMAN DNA-dependent protei5,01Melanoma-associated antigen B2 MAGEB2 sp|O15479|MAGB2_HUMAN Melanoma-associated antigen B2 OS=Homo sapiens GN=MAGEB2 PE=1 SV=34,98

Page 37: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Programmed cell death protein 4 PDCD4 sp|Q53EL6-2|PDCD4_HUMAN Isoform 2 of Programmed cell death protein 4 OS=Homo sapiens GN=PDCD4;sp|Q53EL6|PDCD4_HUMAN Programmed cell death protein 4 OS=Homo sapiens GN=PDCD4 PE=1 SV=24,92Myb-binding protein 1A MYBBP1A sp|Q9BQG0|MBB1A_HUMAN Myb-binding protein 1A OS=Homo sapiens GN=MYBBP1A PE=1 SV=2;sp|Q9BQG0-2|MBB1A_HUMAN Isoform 2 of Myb-binding protein 1A OS=Homo sapiens GN=MYBBP1A;tr|I3L1L3|I3L1L3_HUMAN Myb-binding protein 1A (Fragment) OS=Homo sapiens GN=MYBBP1A PE=4,88ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3YDDX3X;DDX3Y sp|O00571-2|DDX3X_HUMAN Isoform 2 of ATP-dependent RNA helicase DDX3X OS=Homo sapiens GN=DDX3X;sp|O00571|DDX3X_HUMAN ATP-dependent RNA helicase DDX3X OS=Homo sapiens GN=DDX3X PE=1 SV=3;tr|B4DXX7|B4DXX7_HUMAN Uncharacterized protein OS=Homo sapiens GN=DDX3Y4,87Splicing factor 3B subunit 1 SF3B1 sp|O75533|SF3B1_HUMAN Splicing factor 3B subunit 1 OS=Homo sapiens GN=SF3B1 PE=1 SV=34,86General transcription factor 3C polypeptide 1GTF3C1 sp|Q12789-3|TF3C1_HUMAN Isoform 2 of General transcription factor 3C polypeptide 1 OS=Homo sapiens GN=GTF3C1;sp|Q12789|TF3C1_HUMAN General transcription factor 3C polypeptide 1 OS=Homo sapiens GN=GTF3C1 PE=1 SV=44,86RNA-binding protein 39 RNPC2;RBM39 tr|E1P5S2|E1P5S2_HUMAN RNA-binding protein 39 OS=Homo sapiens GN=RBM39 PE=2 SV=1;sp|Q14498-3|RBM39_HUMAN Isoform 3 of RNA-binding protein 39 OS=Homo sapiens GN=RBM39;sp|Q14498-2|RBM39_HUMAN Isoform 2 of RNA-binding protein 39 OS=Homo sapiens GN=RBM39;sp|Q14,85Histone H3;Histone H3.2;Histone H3.1t;Histone H3.3;Histone H3.1;Histone H3.3CH3F3B;H3F3A;HIST2H3A;HIST3H3;HIST1H3A;H3F3Ctr|K7EMV3|K7EMV3_HUMAN Histone H3 OS=Homo sapiens GN=H3F3B PE=2 SV=1;tr|B4DEB1|B4DEB1_HUMAN Histone H3 OS=Homo sapiens GN=H3F3A PE=2 SV=1;tr|K7EK07|K7EK07_HUMAN Histone H3 (Fragment) OS=Homo sapiens GN=H3F3B PE=2 SV=1;tr|K7ES00|K7ES00_HUMAN Histone H3.3 (F4,84BAG family molecular chaperone regulator 2 BAG2 tr|B4DXE2|B4DXE2_HUMAN BAG family molecular chaperone regulator 2 OS=Homo sapiens GN=BAG2 PE=2 SV=1;sp|O95816|BAG2_HUMAN BAG family molecular chaperone regulator 2 OS=Homo sapiens GN=BAG2 PE=1 SV=14,84U5 small nuclear ribonucleoprotein 200 kDa helicaseSNRNP200 sp|O75643|U520_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase OS=Homo sapiens GN=SNRNP200 PE=1 SV=2;tr|C9JAQ9|C9JAQ9_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase OS=Homo sapiens GN=SNRNP200 PE=2 SV=2;sp|O75643-2|U520_HUMAN Isoform 24,83E3 ubiquitin-protein ligase RING2;E3 ubiquitin-protein ligase RING1RNF2;RING1 sp|Q99496|RING2_HUMAN E3 ubiquitin-protein ligase RING2 OS=Homo sapiens GN=RNF2 PE=1 SV=1;sp|Q06587-2|RING1_HUMAN Isoform 2 of E3 ubiquitin-protein ligase RING1 OS=Homo sapiens GN=RING1;sp|Q06587|RING1_HUMAN E3 ubiquitin-protein ligase RING1 OS=Homo sapien4,82AT-hook DNA-binding motif-containing protein 1AHDC1 sp|Q5TGY3|AHDC1_HUMAN AT-hook DNA-binding motif-containing protein 1 OS=Homo sapiens GN=AHDC1 PE=1 SV=14,79Protein S100-A2 S100A2 tr|R4GN49|R4GN49_HUMAN Protein S100-A2 OS=Homo sapiens GN=S100A2 PE=4 SV=1;sp|P29034|S10A2_HUMAN Protein S100-A2 OS=Homo sapiens GN=S100A2 PE=1 SV=34,70Spermatogenesis-associated serine-rich protein 2SPATS2 sp|Q86XZ4|SPAS2_HUMAN Spermatogenesis-associated serine-rich protein 2 OS=Homo sapiens GN=SPATS2 PE=1 SV=1;tr|F8VS10|F8VS10_HUMAN Spermatogenesis-associated serine-rich protein 2 OS=Homo sapiens GN=SPATS2 PE=2 SV=14,65DnaJ homolog subfamily A member 1 DNAJA1 sp|P31689|DNJA1_HUMAN DnaJ homolog subfamily A member 1 OS=Homo sapiens GN=DNAJA1 PE=1 SV=2;tr|B7Z5C0|B7Z5C0_HUMAN DnaJ homolog subfamily A member 1 OS=Homo sapiens GN=DNAJA1 PE=2 SV=1;sp|P31689-2|DNJA1_HUMAN Isoform 2 of DnaJ homolog subfamily A member 1 4,64Polypyrimidine tract-binding protein 1 PTBP1 sp|P26599|PTBP1_HUMAN Polypyrimidine tract-binding protein 1 OS=Homo sapiens GN=PTBP1 PE=1 SV=1;sp|P26599-2|PTBP1_HUMAN Isoform 2 of Polypyrimidine tract-binding protein 1 OS=Homo sapiens GN=PTBP1;sp|P26599-3|PTBP1_HUMAN Isoform 3 of Polypyrimidine tract-b4,63Periodic tryptophan protein 2 homolog PWP2 sp|Q15269|PWP2_HUMAN Periodic tryptophan protein 2 homolog OS=Homo sapiens GN=PWP2 PE=1 SV=24,53Thymidine kinase;Thymidine kinase, cytosolicTK1 tr|K7ES52|K7ES52_HUMAN Thymidine kinase OS=Homo sapiens GN=TK1 PE=2 SV=1;tr|K7ERJ1|K7ERJ1_HUMAN Thymidine kinase (Fragment) OS=Homo sapiens GN=TK1 PE=2 SV=1;tr|K7ERV3|K7ERV3_HUMAN Thymidine kinase OS=Homo sapiens GN=TK1 PE=2 SV=1;sp|P04183|KITH_HUMAN Thymi4,46H/ACA ribonucleoprotein complex subunit 1 GAR1 sp|Q9NY12-2|GAR1_HUMAN Isoform 2 of H/ACA ribonucleoprotein complex subunit 1 OS=Homo sapiens GN=GAR1;sp|Q9NY12|GAR1_HUMAN H/ACA ribonucleoprotein complex subunit 1 OS=Homo sapiens GN=GAR1 PE=1 SV=14,38Cytoplasmic FMR1-interacting protein 1;Cytoplasmic FMR1-interacting protein 2CYFIP1;CYFIP2 sp|Q7L576|CYFP1_HUMAN Cytoplasmic FMR1-interacting protein 1 OS=Homo sapiens GN=CYFIP1 PE=1 SV=1;tr|H7C229|H7C229_HUMAN Cytoplasmic FMR1-interacting protein 2 OS=Homo sapiens GN=CYFIP2 PE=2 SV=1;tr|E7EW33|E7EW33_HUMAN Cytoplasmic FMR1-interacting protein 24,37Trifunctional enzyme subunit beta, mitochondrial;3-ketoacyl-CoA thiolaseHADHB tr|B4E2W0|B4E2W0_HUMAN 3-ketoacyl-CoA thiolase OS=Homo sapiens GN=HADHB PE=2 SV=1;sp|P55084|ECHB_HUMAN Trifunctional enzyme subunit beta, mitochondrial OS=Homo sapiens GN=HADHB PE=1 SV=3;tr|F5GZQ3|F5GZQ3_HUMAN 3-ketoacyl-CoA thiolase OS=Homo sapiens GN=HAD4,36DNA dC->dU-editing enzyme APOBEC-3B;DNA dC->dU-editing enzyme APOBEC-3AAPOBEC3B;APOBEC3Atr|B0QYD3|B0QYD3_HUMAN DNA dC->dU-editing enzyme APOBEC-3B OS=Homo sapiens GN=APOBEC3B PE=2 SV=1;sp|Q9UH17|ABC3B_HUMAN DNA dC->dU-editing enzyme APOBEC-3B OS=Homo sapiens GN=APOBEC3B PE=1 SV=1;sp|Q9UH17-3|ABC3B_HUMAN Isoform 3 of DNA dC->dU-editing enzyme 4,34Pre-mRNA-processing factor 6 PRPF6 sp|O94906-2|PRP6_HUMAN Isoform 2 of Pre-mRNA-processing factor 6 OS=Homo sapiens GN=PRPF6;sp|O94906|PRP6_HUMAN Pre-mRNA-processing factor 6 OS=Homo sapiens GN=PRPF6 PE=1 SV=14,33Transcription factor A, mitochondrial TFAM tr|H7BYN3|H7BYN3_HUMAN Transcription factor A, mitochondrial (Fragment) OS=Homo sapiens GN=TFAM PE=4 SV=1;sp|Q00059|TFAM_HUMAN Transcription factor A, mitochondrial OS=Homo sapiens GN=TFAM PE=1 SV=1;sp|Q00059-2|TFAM_HUMAN Isoform 2 of Transcription factor 4,3260S ribosomal export protein NMD3 NMD3 tr|C9JA08|C9JA08_HUMAN 60S ribosomal export protein NMD3 OS=Homo sapiens GN=NMD3 PE=2 SV=1;sp|Q96D46|NMD3_HUMAN 60S ribosomal export protein NMD3 OS=Homo sapiens GN=NMD3 PE=1 SV=1;tr|C9IZW9|C9IZW9_HUMAN 60S ribosomal export protein NMD3 (Fragment) OS=Homo 4,31Eukaryotic translation initiation factor 2 subunit 1EIF2S1 sp|P05198|IF2A_HUMAN Eukaryotic translation initiation factor 2 subunit 1 OS=Homo sapiens GN=EIF2S1 PE=1 SV=34,30116 kDa U5 small nuclear ribonucleoprotein componentEFTUD2 sp|Q15029-2|U5S1_HUMAN Isoform 2 of 116 kDa U5 small nuclear ribonucleoprotein component OS=Homo sapiens GN=EFTUD2;tr|K7EJ81|K7EJ81_HUMAN 116 kDa U5 small nuclear ribonucleoprotein component OS=Homo sapiens GN=EFTUD2 PE=2 SV=1;sp|Q15029|U5S1_HUMAN 116 kDa 4,29Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processedEIF4A3 sp|P38919|IF4A3_HUMAN Eukaryotic initiation factor 4A-III OS=Homo sapiens GN=EIF4A3 PE=1 SV=44,27ELM2 and SANT domain-containing protein 1ELMSAN1 tr|F6RU81|F6RU81_HUMAN ELM2 and SANT domain-containing protein 1 (Fragment) OS=Homo sapiens GN=ELMSAN1 PE=2 SV=1;sp|Q6PJG2|EMSA1_HUMAN ELM2 and SANT domain-containing protein 1 OS=Homo sapiens GN=ELMSAN1 PE=1 SV=2;tr|H7C1L3|H7C1L3_HUMAN ELM2 and SANT domai4,27Cytochrome c oxidase subunit NDUFA4 NDUFA4 sp|O00483|NDUA4_HUMAN NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4 OS=Homo sapiens GN=NDUFA4 PE=1 SV=14,23TATA-binding protein-associated factor 2N TAF15 sp|Q92804-2|RBP56_HUMAN Isoform Short of TATA-binding protein-associated factor 2N OS=Homo sapiens GN=TAF15;sp|Q92804|RBP56_HUMAN TATA-binding protein-associated factor 2N OS=Homo sapiens GN=TAF15 PE=1 SV=1;tr|K7EN07|K7EN07_HUMAN TATA-binding protein-assoc4,20Nucleosome assembly protein 1-like 1 NAP1L1 tr|H0YHC3|H0YHC3_HUMAN Nucleosome assembly protein 1-like 1 (Fragment) OS=Homo sapiens GN=NAP1L1 PE=2 SV=1;tr|F8W020|F8W020_HUMAN Nucleosome assembly protein 1-like 1 (Fragment) OS=Homo sapiens GN=NAP1L1 PE=2 SV=1;tr|F8W118|F8W118_HUMAN Nucleosome assembly4,19Importin-5 IPO5 tr|H0Y8C6|H0Y8C6_HUMAN Importin-5 (Fragment) OS=Homo sapiens GN=IPO5 PE=4 SV=1;sp|O00410|IPO5_HUMAN Importin-5 OS=Homo sapiens GN=IPO5 PE=1 SV=4;sp|O00410-3|IPO5_HUMAN Isoform 3 of Importin-5 OS=Homo sapiens GN=IPO5;tr|B4E0R6|B4E0R6_HUMAN Importin-5 OS=Hom4,16Eukaryotic translation initiation factor 3 subunit MEIF3M sp|Q7L2H7|EIF3M_HUMAN Eukaryotic translation initiation factor 3 subunit M OS=Homo sapiens GN=EIF3M PE=1 SV=1;tr|J3KNJ2|J3KNJ2_HUMAN Eukaryotic translation initiation factor 3 subunit M (Fragment) OS=Homo sapiens GN=EIF3M PE=2 SV=1;tr|B4E2Q4|B4E2Q4_HUMAN E4,15Eukaryotic translation elongation factor 1 epsilon-1EEF1E1;EEF1E1-BLOC1S5tr|H0YAL7|H0YAL7_HUMAN Eukaryotic translation elongation factor 1 epsilon-1 (Fragment) OS=Homo sapiens GN=EEF1E1 PE=4 SV=1;tr|D6RBD7|D6RBD7_HUMAN Eukaryotic translation elongation factor 1 epsilon-1 OS=Homo sapiens GN=EEF1E1 PE=2 SV=1;tr|C9J1V9|C9J1V9_HUMA4,14NHP2-like protein 1;NHP2-like protein 1, N-terminally processedNHP2L1 tr|B1AHD1|B1AHD1_HUMAN NHP2-like protein 1 OS=Homo sapiens GN=NHP2L1 PE=2 SV=1;sp|P55769|NH2L1_HUMAN NHP2-like protein 1 OS=Homo sapiens GN=NHP2L1 PE=1 SV=34,12Complement component 1 Q subcomponent-binding protein, mitochondrialC1QBP sp|Q07021|C1QBP_HUMAN Complement component 1 Q subcomponent-binding protein, mitochondrial OS=Homo sapiens GN=C1QBP PE=1 SV=1;tr|I3L3Q7|I3L3Q7_HUMAN Complement component 1 Q subcomponent-binding protein, mitochondrial (Fragment) OS=Homo sapiens GN=C1QBP PE4,12DNA topoisomerase 2-beta;DNA topoisomerase 2TOP2B sp|Q02880-2|TOP2B_HUMAN Isoform Beta-1 of DNA topoisomerase 2-beta OS=Homo sapiens GN=TOP2B;sp|Q02880|TOP2B_HUMAN DNA topoisomerase 2-beta OS=Homo sapiens GN=TOP2B PE=1 SV=3;tr|E9PCY5|E9PCY5_HUMAN DNA topoisomerase 2 (Fragment) OS=Homo sapiens GN=TOP2B PE=4,02Ankyrin repeat domain-containing protein 17;Ankyrin repeat and KH domain-containing protein 1ANKRD17;ANKHD1 tr|H0YM23|H0YM23_HUMAN Ankyrin repeat domain-containing protein 17 (Fragment) OS=Homo sapiens GN=ANKRD17 PE=4 SV=1;sp|O75179-6|ANR17_HUMAN Isoform 6 of Ankyrin repeat domain-containing protein 17 OS=Homo sapiens GN=ANKRD17;tr|E7EUV3|E7EUV3_HUMAN Ankyrin re4,01Ribosomal RNA processing protein 1 homolog BRRP1B sp|Q14684-2|RRP1B_HUMAN Isoform 2 of Ribosomal RNA processing protein 1 homolog B OS=Homo sapiens GN=RRP1B;sp|Q14684|RRP1B_HUMAN Ribosomal RNA processing protein 1 homolog B OS=Homo sapiens GN=RRP1B PE=1 SV=34,00Pre-rRNA-processing protein TSR1 homolog TSR1 sp|Q2NL82|TSR1_HUMAN Pre-rRNA-processing protein TSR1 homolog OS=Homo sapiens GN=TSR1 PE=1 SV=13,99TRMT1-like protein TRMT1L sp|Q7Z2T5|TRM1L_HUMAN TRMT1-like protein OS=Homo sapiens GN=TRMT1L PE=1 SV=23,96Luc7-like protein 3 LUC7L3 tr|B4DJ96|B4DJ96_HUMAN Luc7-like protein 3 OS=Homo sapiens GN=LUC7L3 PE=2 SV=1;tr|J3KPP4|J3KPP4_HUMAN Cisplatin resistance-associated overexpressed protein, isoform CRA_b OS=Homo sapiens GN=LUC7L3 PE=2 SV=1;sp|O95232|LC7L3_HUMAN Luc7-like protein 3 OS=Homo3,90Mitochondrial import inner membrane translocase subunit TIM50TIMM50 tr|M0R0C3|M0R0C3_HUMAN Mitochondrial import inner membrane translocase subunit TIM50 (Fragment) OS=Homo sapiens GN=TIMM50 PE=4 SV=1;tr|M0R2F8|M0R2F8_HUMAN Mitochondrial import inner membrane translocase subunit TIM50 OS=Homo sapiens GN=TIMM50 PE=4 SV=2;sp|3,89Protein arginine N-methyltransferase 1 PRMT1 tr|E9PKG1|E9PKG1_HUMAN Protein arginine N-methyltransferase 1 OS=Homo sapiens GN=PRMT1 PE=2 SV=1;tr|H7C2I1|H7C2I1_HUMAN Protein arginine N-methyltransferase 1 OS=Homo sapiens GN=PRMT1 PE=2 SV=1;sp|Q99873-3|ANM1_HUMAN Isoform 3 of Protein arginine N-methylt3,88Heat shock cognate 71 kDa protein HSPA8 sp|P11142|HSP7C_HUMAN Heat shock cognate 71 kDa protein OS=Homo sapiens GN=HSPA8 PE=1 SV=1;tr|E9PKE3|E9PKE3_HUMAN Heat shock cognate 71 kDa protein OS=Homo sapiens GN=HSPA8 PE=2 SV=1;sp|P11142-2|HSP7C_HUMAN Isoform 2 of Heat shock cognate 71 kDa protein OS3,86Abl interactor 1 ABI1 tr|F5H1G9|F5H1G9_HUMAN Abl interactor 1 OS=Homo sapiens GN=ABI1 PE=2 SV=1;tr|F8WA55|F8WA55_HUMAN Abl interactor 1 OS=Homo sapiens GN=ABI1 PE=2 SV=1;tr|F8WA56|F8WA56_HUMAN Abl interactor 1 OS=Homo sapiens GN=ABI1 PE=2 SV=1;tr|A6NFN2|A6NFN2_HUMAN Abl interac3,85Brain-specific angiogenesis inhibitor 1-associated protein 2BAIAP2 sp|Q9UQB8-2|BAIP2_HUMAN Isoform 2 of Brain-specific angiogenesis inhibitor 1-associated protein 2 OS=Homo sapiens GN=BAIAP2;sp|Q9UQB8|BAIP2_HUMAN Brain-specific angiogenesis inhibitor 1-associated protein 2 OS=Homo sapiens GN=BAIAP2 PE=1 SV=1;tr|F8W878|F8W3,81Splicing factor U2AF 65 kDa subunit U2AF2 tr|K7ENG2|K7ENG2_HUMAN Splicing factor U2AF 65 kDa subunit OS=Homo sapiens GN=U2AF2 PE=2 SV=1;sp|P26368-2|U2AF2_HUMAN Isoform 2 of Splicing factor U2AF 65 kDa subunit OS=Homo sapiens GN=U2AF2;sp|P26368|U2AF2_HUMAN Splicing factor U2AF 65 kDa subunit OS=Hom3,81Guanine nucleotide-binding protein G(s) subunit alpha isoforms short;Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas;Guanine nucleotide-binding protein G(t) subunit alpha-1;Guanine nucleotide-binding protein G(i) subunit alpha-1;Guanine nucleotide-binding protein G(t) subunit alpha-2;Guanine nucleotide-binding protein G(o) subunit alpha;Guanine nucleotide-binding protein G(k) subunit alpha;Guanine nucleotide-binding protein G(t) subunit alpha-3;Guanine nucleotide-binding protein G(i) subunit alpha-2;Guanine nucleotide-binding protein G(olf) subunit alphaGNAS;GNAT1;GNAI1;GNAT2;GNAO1;GNAI3;GNAT3;GNAI2;GNALsp|P63092-3|GNAS2_HUMAN Isoform 3 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short OS=Homo sapiens GN=GNAS;sp|P63092-2|GNAS2_HUMAN Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short OS=Homo sapiens3,80Signal recognition particle subunit SRP68 SRP68 sp|Q9UHB9-4|SRP68_HUMAN Isoform 4 of Signal recognition particle subunit SRP68 OS=Homo sapiens GN=SRP68;sp|Q9UHB9|SRP68_HUMAN Signal recognition particle subunit SRP68 OS=Homo sapiens GN=SRP68 PE=1 SV=2;tr|F5H5Y3|F5H5Y3_HUMAN Signal recognition particle su3,79Uncharacterized protein KIAA1522 KIAA1522 sp|Q9P206-2|K1522_HUMAN Isoform 2 of Uncharacterized protein KIAA1522 OS=Homo sapiens GN=KIAA15223,76Eukaryotic translation initiation factor 4 gamma 2EIF4G2 tr|D3DQV9|D3DQV9_HUMAN Eukaryotic translation initiation factor 4 gamma 2 (Fragment) OS=Homo sapiens GN=EIF4G2 PE=2 SV=1;sp|P78344|IF4G2_HUMAN Eukaryotic translation initiation factor 4 gamma 2 OS=Homo sapiens GN=EIF4G2 PE=1 SV=1;tr|H0YEC5|H0YEC5_HUMAN Euk3,75Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenaseHADHA sp|P40939|ECHA_HUMAN Trifunctional enzyme subunit alpha, mitochondrial OS=Homo sapiens GN=HADHA PE=1 SV=23,75Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processedHNRNPF sp|P52597|HNRPF_HUMAN Heterogeneous nuclear ribonucleoprotein F OS=Homo sapiens GN=HNRNPF PE=1 SV=33,73RNA-binding protein EWS EWSR1 tr|B0QYK0|B0QYK0_HUMAN RNA-binding protein EWS OS=Homo sapiens GN=EWSR1 PE=2 SV=1;sp|Q01844-6|EWS_HUMAN Isoform 6 of RNA-binding protein EWS OS=Homo sapiens GN=EWSR1;sp|Q01844-3|EWS_HUMAN Isoform 3 of RNA-binding protein EWS OS=Homo sapiens GN=EWSR1;sp|Q013,72Tetratricopeptide repeat protein 37 TTC37 sp|Q6PGP7|TTC37_HUMAN Tetratricopeptide repeat protein 37 OS=Homo sapiens GN=TTC37 PE=1 SV=13,67

Page 38: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunitOGT sp|O15294|OGT1_HUMAN UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit OS=Homo sapiens GN=OGT PE=1 SV=3;sp|O15294-4|OGT1_HUMAN Isoform 4 of UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit OS=H3,64Probable helicase senataxin SETX sp|Q7Z333|SETX_HUMAN Probable helicase senataxin OS=Homo sapiens GN=SETX PE=1 SV=4;sp|Q7Z333-4|SETX_HUMAN Isoform 4 of Probable helicase senataxin OS=Homo sapiens GN=SETX;sp|Q7Z333-3|SETX_HUMAN Isoform 3 of Probable helicase senataxin OS=Homo sapiens GN=SE3,58SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1SMARCB1 tr|G5E975|G5E975_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1, isoform CRA_c OS=Homo sapiens GN=SMARCB1 PE=2 SV=1;sp|Q12824-2|SNF5_HUMAN Isoform B of SWI/SNF-related matrix-associated actin-depende3,55Poly [ADP-ribose] polymerase 1 PARP1 sp|P09874|PARP1_HUMAN Poly [ADP-ribose] polymerase 1 OS=Homo sapiens GN=PARP1 PE=1 SV=43,54Nuclear mitotic apparatus protein 1 NUMA1 tr|H0YFY6|H0YFY6_HUMAN Nuclear mitotic apparatus protein 1 (Fragment) OS=Homo sapiens GN=NUMA1 PE=4 SV=1;sp|Q14980-2|NUMA1_HUMAN Isoform 2 of Nuclear mitotic apparatus protein 1 OS=Homo sapiens GN=NUMA1;sp|Q14980|NUMA1_HUMAN Nuclear mitotic apparatus prote3,53D-3-phosphoglycerate dehydrogenase PHGDH sp|O43175|SERA_HUMAN D-3-phosphoglycerate dehydrogenase OS=Homo sapiens GN=PHGDH PE=1 SV=4;tr|Q5SZU1|Q5SZU1_HUMAN D-3-phosphoglycerate dehydrogenase OS=Homo sapiens GN=PHGDH PE=2 SV=13,51Casein kinase II subunit alpha 3;Casein kinase II subunit alphaCSNK2A1;CSNK2A3tr|E7EU96|E7EU96_HUMAN Casein kinase II subunit alpha OS=Homo sapiens GN=CSNK2A1 PE=2 SV=1;sp|Q8NEV1|CSK23_HUMAN Casein kinase II subunit alpha 3 OS=Homo sapiens GN=CSNK2A3 PE=1 SV=2;sp|P68400|CSK21_HUMAN Casein kinase II subunit alpha OS=Homo sapiens GN=C3,50Nck-associated protein 1 NCKAP1 sp|Q9Y2A7|NCKP1_HUMAN Nck-associated protein 1 OS=Homo sapiens GN=NCKAP1 PE=1 SV=1;sp|Q9Y2A7-2|NCKP1_HUMAN Isoform 2 of Nck-associated protein 1 OS=Homo sapiens GN=NCKAP13,49Myosin light polypeptide 6 MYL6 tr|F8W1R7|F8W1R7_HUMAN Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=2 SV=1;tr|J3KND3|J3KND3_HUMAN Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=2 SV=1;tr|G8JLA2|G8JLA2_HUMAN Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=2 SV=1;tr|G3,48T-complex protein 1 subunit gamma CCT3 tr|B4DUR8|B4DUR8_HUMAN T-complex protein 1 subunit gamma OS=Homo sapiens GN=CCT3 PE=2 SV=1;sp|P49368-2|TCPG_HUMAN Isoform 2 of T-complex protein 1 subunit gamma OS=Homo sapiens GN=CCT3;sp|P49368|TCPG_HUMAN T-complex protein 1 subunit gamma OS=Homo sapiens 3,46Unconventional myosin-Ic MYO1C tr|F5H6E2|F5H6E2_HUMAN Unconventional myosin-Ic OS=Homo sapiens GN=MYO1C PE=2 SV=1;sp|O00159-2|MYO1C_HUMAN Isoform 2 of Unconventional myosin-Ic OS=Homo sapiens GN=MYO1C;sp|O00159-3|MYO1C_HUMAN Isoform 3 of Unconventional myosin-Ic OS=Homo sapiens GN=MYO1C3,403-hydroxyacyl-CoA dehydrogenase type-2 HSD17B10 sp|Q99714|HCD2_HUMAN 3-hydroxyacyl-CoA dehydrogenase type-2 OS=Homo sapiens GN=HSD17B10 PE=1 SV=3;sp|Q99714-2|HCD2_HUMAN Isoform 2 of 3-hydroxyacyl-CoA dehydrogenase type-2 OS=Homo sapiens GN=HSD17B10;tr|Q5H928|Q5H928_HUMAN 3-hydroxyacyl-CoA dehydrogenase 3,39Microtubule-associated protein;Microtubule-associated protein 4MAP4 tr|E7EVA0|E7EVA0_HUMAN Microtubule-associated protein OS=Homo sapiens GN=MAP4 PE=2 SV=1;sp|P27816-6|MAP4_HUMAN Isoform 6 of Microtubule-associated protein 4 OS=Homo sapiens GN=MAP4;sp|P27816|MAP4_HUMAN Microtubule-associated protein 4 OS=Homo sapiens GN=MA3,36Cystathionine beta-synthase CBS tr|F5H2U1|F5H2U1_HUMAN Cystathionine beta-synthase OS=Homo sapiens GN=CBS PE=2 SV=1;sp|P35520|CBS_HUMAN Cystathionine beta-synthase OS=Homo sapiens GN=CBS PE=1 SV=2;sp|P35520-2|CBS_HUMAN Isoform 2 of Cystathionine beta-synthase OS=Homo sapiens GN=CBS;tr|C93,34NEDD4-like E3 ubiquitin-protein ligase WWP2WWP2 sp|O00308-2|WWP2_HUMAN Isoform 2 of NEDD4-like E3 ubiquitin-protein ligase WWP2 OS=Homo sapiens GN=WWP23,32Signal transducer and activator of transcription 3;Signal transducer and activator of transcriptionSTAT3 tr|K7ENL3|K7ENL3_HUMAN Signal transducer and activator of transcription OS=Homo sapiens GN=STAT3 PE=2 SV=1;sp|P40763-2|STAT3_HUMAN Isoform Del-701 of Signal transducer and activator of transcription 3 OS=Homo sapiens GN=STAT3;sp|P40763|STAT3_HUMAN Signal t3,29LINE-1 retrotransposable element ORF1 proteinL1RE1 sp|Q9UN81|LORF1_HUMAN LINE-1 retrotransposable element ORF1 protein OS=Homo sapiens GN=L1RE1 PE=1 SV=13,29RNA-binding protein Raly RALY tr|Q5QPM0|Q5QPM0_HUMAN RNA-binding protein Raly (Fragment) OS=Homo sapiens GN=RALY PE=2 SV=1;tr|Q5QPM1|Q5QPM1_HUMAN RNA-binding protein Raly (Fragment) OS=Homo sapiens GN=RALY PE=2 SV=1;tr|Q5QPL9|Q5QPL9_HUMAN RNA-binding protein Raly (Fragment) OS=Homo sap3,27RNA-binding protein 10 RBM10 sp|P98175-4|RBM10_HUMAN Isoform 4 of RNA-binding protein 10 OS=Homo sapiens GN=RBM10;sp|P98175-3|RBM10_HUMAN Isoform 3 of RNA-binding protein 10 OS=Homo sapiens GN=RBM10;sp|P98175-2|RBM10_HUMAN Isoform 2 of RNA-binding protein 10 OS=Homo sapiens GN=RBM10;s3,27Ras GTPase-activating-like protein IQGAP1 IQGAP1 sp|P46940|IQGA1_HUMAN Ras GTPase-activating-like protein IQGAP1 OS=Homo sapiens GN=IQGAP1 PE=1 SV=1;tr|H0YLE8|H0YLE8_HUMAN Ras GTPase-activating-like protein IQGAP1 OS=Homo sapiens GN=IQGAP1 PE=2 SV=13,25Nuclear fragile X mental retardation-interacting protein 2NUFIP2 sp|Q7Z417|NUFP2_HUMAN Nuclear fragile X mental retardation-interacting protein 2 OS=Homo sapiens GN=NUFIP2 PE=1 SV=13,24BolA-like protein 2 BOLA2;BOLA2B sp|Q9H3K6|BOLA2_HUMAN BolA-like protein 2 OS=Homo sapiens GN=BOLA2 PE=1 SV=1;tr|H3BV85|H3BV85_HUMAN BolA-like protein 2 (Fragment) OS=Homo sapiens GN=BOLA2B PE=2 SV=1;tr|H3BTW0|H3BTW0_HUMAN BolA-like protein 2 (Fragment) OS=Homo sapiens GN=BOLA2 PE=2 SV=1;3,21Heat shock protein HSP 90-alpha HSP90AA1 sp|P07900|HS90A_HUMAN Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1 PE=1 SV=5;sp|P07900-2|HS90A_HUMAN Isoform 2 of Heat shock protein HSP 90-alpha OS=Homo sapiens GN=HSP90AA1;tr|Q86U12|Q86U12_HUMAN Full-length cDNA clone CS0CAP007YF18 of Thym3,21Zinc finger CCCH-type antiviral protein 1-like ZC3HAV1L sp|Q96H79|ZCCHL_HUMAN Zinc finger CCCH-type antiviral protein 1-like OS=Homo sapiens GN=ZC3HAV1L PE=1 SV=23,20Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2RPN2 tr|Q5JYR4|Q5JYR4_HUMAN Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (Fragment) OS=Homo sapiens GN=RPN2 PE=2 SV=1;tr|Q5JYR7|Q5JYR7_HUMAN Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 (Fragment) OS=Homo 3,19MAP7 domain-containing protein 1 MAP7D1 sp|Q3KQU3-2|MA7D1_HUMAN Isoform 2 of MAP7 domain-containing protein 1 OS=Homo sapiens GN=MAP7D1;sp|Q3KQU3-4|MA7D1_HUMAN Isoform 4 of MAP7 domain-containing protein 1 OS=Homo sapiens GN=MAP7D1;sp|Q3KQU3|MA7D1_HUMAN MAP7 domain-containing protein 1 OS=Homo s3,17Phosphate carrier protein, mitochondrial SLC25A3 sp|Q00325-2|MPCP_HUMAN Isoform B of Phosphate carrier protein, mitochondrial OS=Homo sapiens GN=SLC25A3;sp|Q00325|MPCP_HUMAN Phosphate carrier protein, mitochondrial OS=Homo sapiens GN=SLC25A3 PE=1 SV=2;tr|F8VVM2|F8VVM2_HUMAN Phosphate carrier protein, mit3,16Calmodulin CALM1;CALM2;CALM3tr|E7ETZ0|E7ETZ0_HUMAN Calmodulin OS=Homo sapiens GN=CALM1 PE=2 SV=1;tr|H0Y7A7|H0Y7A7_HUMAN Calmodulin (Fragment) OS=Homo sapiens GN=CALM2 PE=2 SV=1;tr|E7EMB3|E7EMB3_HUMAN Calmodulin OS=Homo sapiens GN=CALM2 PE=2 SV=1;sp|P62158|CALM_HUMAN Calmodulin OS=Hom3,13Suppressor of SWI4 1 homolog PPAN tr|H7C446|H7C446_HUMAN Suppressor of SWI4 1 homolog (Fragment) OS=Homo sapiens GN=PPAN PE=4 SV=1;tr|A8MV53|A8MV53_HUMAN HCG2033702, isoform CRA_a OS=Homo sapiens GN=PPAN PE=2 SV=1;sp|Q9NQ55-2|SSF1_HUMAN Isoform 2 of Suppressor of SWI4 1 homolog OS=Homo sap3,11Exosome complex component RRP40 EXOSC3 sp|Q9NQT5-2|EXOS3_HUMAN Isoform 2 of Exosome complex component RRP40 OS=Homo sapiens GN=EXOSC3;sp|Q9NQT5|EXOS3_HUMAN Exosome complex component RRP40 OS=Homo sapiens GN=EXOSC3 PE=1 SV=33,10Serine/arginine repetitive matrix protein 2 SRRM2 sp|Q9UQ35|SRRM2_HUMAN Serine/arginine repetitive matrix protein 2 OS=Homo sapiens GN=SRRM2 PE=1 SV=23,10Wiskott-Aldrich syndrome protein family member 2WASF2 sp|Q9Y6W5|WASF2_HUMAN Wiskott-Aldrich syndrome protein family member 2 OS=Homo sapiens GN=WASF2 PE=1 SV=3;sp|Q9Y6W5-2|WASF2_HUMAN Isoform 2 of Wiskott-Aldrich syndrome protein family member 2 OS=Homo sapiens GN=WASF23,09Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6HCFC1 tr|A6NEM2|A6NEM2_HUMAN HCF N-terminal chain 5 OS=Homo sapiens GN=HCFC1 PE=2 SV=2;sp|P51610-2|HCFC1_HUMAN Isoform 2 of Host cell factor 1 OS=Homo sapiens GN=HCFC1;sp|P51610|HCFC1_HUMAN Host cell factor 1 OS=Homo sapiens GN=HCFC1 PE=1 SV=2;sp|P51610-4|HCFC1_3,09Double-stranded RNA-binding protein Staufen homolog 2STAU2 tr|E5RJN7|E5RJN7_HUMAN Double-stranded RNA-binding protein Staufen homolog 2 (Fragment) OS=Homo sapiens GN=STAU2 PE=2 SV=1;tr|F8VPI7|F8VPI7_HUMAN Double-stranded RNA-binding protein Staufen homolog 2 OS=Homo sapiens GN=STAU2 PE=2 SV=1;tr|E7EPX0|E7EPX0_HUMA3,05E3 ubiquitin/ISG15 ligase TRIM25 TRIM25 sp|Q14258|TRI25_HUMAN E3 ubiquitin/ISG15 ligase TRIM25 OS=Homo sapiens GN=TRIM25 PE=1 SV=23,02Elongation factor 2 EEF2 sp|P13639|EF2_HUMAN Elongation factor 2 OS=Homo sapiens GN=EEF2 PE=1 SV=43,00Structural maintenance of chromosomes protein 1ASMC1A sp|Q14683|SMC1A_HUMAN Structural maintenance of chromosomes protein 1A OS=Homo sapiens GN=SMC1A PE=1 SV=2;tr|H0Y7K8|H0Y7K8_HUMAN Structural maintenance of chromosomes protein 1A (Fragment) OS=Homo sapiens GN=SMC1A PE=4 SV=2;tr|V9GY57|V9GY57_HUMAN Structura2,99Protein transport protein Sec24C SEC24C tr|E7EP00|E7EP00_HUMAN Protein transport protein Sec24C OS=Homo sapiens GN=SEC24C PE=2 SV=2;tr|G5EA31|G5EA31_HUMAN Protein transport protein Sec24C OS=Homo sapiens GN=SEC24C PE=2 SV=1;sp|P53992|SC24C_HUMAN Protein transport protein Sec24C OS=Homo sapiens G2,9778 kDa glucose-regulated protein HSPA5 sp|P11021|GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=22,96Multifunctional methyltransferase subunit TRM112-like proteinTRMT112 tr|F5GX77|F5GX77_HUMAN tRNA methyltransferase 112 homolog OS=Homo sapiens GN=TRMT112 PE=2 SV=1;tr|M0R242|M0R242_HUMAN Uncharacterized protein OS=Homo sapiens PE=4 SV=1;tr|J3KNG5|J3KNG5_HUMAN tRNA methyltransferase 112 homolog OS=Homo sapiens GN=TRMT112 PE=2,94Poly(rC)-binding protein 1 PCBP1 sp|Q15365|PCBP1_HUMAN Poly(rC)-binding protein 1 OS=Homo sapiens GN=PCBP1 PE=1 SV=22,93Heat shock protein 105 kDa HSPH1 sp|Q92598-2|HS105_HUMAN Isoform Beta of Heat shock protein 105 kDa OS=Homo sapiens GN=HSPH1;sp|Q92598-3|HS105_HUMAN Isoform 3 of Heat shock protein 105 kDa OS=Homo sapiens GN=HSPH1;sp|Q92598|HS105_HUMAN Heat shock protein 105 kDa OS=Homo sapiens GN=HSPH1 P2,92Putative RNA-binding protein Luc7-like 1 LUC7L tr|B8ZZ10|B8ZZ10_HUMAN LUC7-like (S. cerevisiae) (Fragment) OS=Homo sapiens GN=LUC7L PE=2 SV=1;tr|A8MYV2|A8MYV2_HUMAN LUC7-like (S. cerevisiae) OS=Homo sapiens GN=LUC7L PE=2 SV=1;sp|Q9NQ29-2|LUC7L_HUMAN Isoform 2 of Putative RNA-binding protein Luc7-like 12,91Arrestin domain-containing protein 1 ARRDC1 sp|Q8N5I2|ARRD1_HUMAN Arrestin domain-containing protein 1 OS=Homo sapiens GN=ARRDC1 PE=2 SV=12,86Growth factor receptor-bound protein 2 GRB2 sp|P62993|GRB2_HUMAN Growth factor receptor-bound protein 2 OS=Homo sapiens GN=GRB2 PE=1 SV=1;tr|J3KT38|J3KT38_HUMAN Growth factor receptor-bound protein 2 (Fragment) OS=Homo sapiens GN=GRB2 PE=2 SV=1;tr|J3QRL5|J3QRL5_HUMAN Growth factor receptor-bound pro2,84C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processedMTHFD1 tr|F5H2F4|F5H2F4_HUMAN C-1-tetrahydrofolate synthase, cytoplasmic OS=Homo sapiens GN=MTHFD1 PE=2 SV=1;sp|P11586|C1TC_HUMAN C-1-tetrahydrofolate synthase, cytoplasmic OS=Homo sapiens GN=MTHFD1 PE=1 SV=32,82Cell division cycle 5-like protein CDC5L sp|Q99459|CDC5L_HUMAN Cell division cycle 5-like protein OS=Homo sapiens GN=CDC5L PE=1 SV=22,81Kinectin KTN1 sp|Q86UP2-2|KTN1_HUMAN Isoform 2 of Kinectin OS=Homo sapiens GN=KTN1;sp|Q86UP2-3|KTN1_HUMAN Isoform 3 of Kinectin OS=Homo sapiens GN=KTN1;sp|Q86UP2|KTN1_HUMAN Kinectin OS=Homo sapiens GN=KTN1 PE=1 SV=1;tr|G3V4Y7|G3V4Y7_HUMAN Kinectin OS=Homo sapiens GN=KTN2,79Cysteine--tRNA ligase, cytoplasmic CARS tr|A8MVQ3|A8MVQ3_HUMAN Cysteine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=CARS PE=2 SV=1;tr|B4DKY1|B4DKY1_HUMAN Cysteine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=CARS PE=2 SV=1;sp|P49589-2|SYCC_HUMAN Isoform 2 of Cysteine--tRNA ligase, cytoplasmic O2,79Tricarboxylate transport protein, mitochondrialSLC25A1 sp|P53007|TXTP_HUMAN Tricarboxylate transport protein, mitochondrial OS=Homo sapiens GN=SLC25A1 PE=1 SV=2;tr|B4DP62|B4DP62_HUMAN Solute carrier family 25 (Mitochondrial carrier; citrate transporter), member 1, isoform CRA_b OS=Homo sapiens GN=SLC25A1 PE=2 2,78Dihydropyrimidinase-related protein 3 DPYSL3 sp|Q14195-2|DPYL3_HUMAN Isoform LCRMP-4 of Dihydropyrimidinase-related protein 3 OS=Homo sapiens GN=DPYSL3;tr|F5GWI3|F5GWI3_HUMAN Dihydropyrimidinase-related protein 3 OS=Homo sapiens GN=DPYSL3 PE=2 SV=1;tr|H0YBT4|H0YBT4_HUMAN Dihydropyrimidinase-related p2,77Methionine--tRNA ligase, cytoplasmic MARS sp|P56192|SYMC_HUMAN Methionine--tRNA ligase, cytoplasmic OS=Homo sapiens GN=MARS PE=1 SV=2;tr|H0YHV5|H0YHV5_HUMAN Methionine--tRNA ligase, cytoplasmic (Fragment) OS=Homo sapiens GN=MARS PE=4 SV=1;tr|B3KVK7|B3KVK7_HUMAN Methionine--tRNA ligase, cytoplasmic2,70Putative RNA-binding protein Luc7-like 2 LUC7L2 sp|Q96HJ9-2|CG055_HUMAN Isoform 2 of UPF0562 protein C7orf55 OS=Homo sapiens GN=C7orf55;sp|Q9Y383-3|LC7L2_HUMAN Isoform 3 of Putative RNA-binding protein Luc7-like 2 OS=Homo sapiens GN=LUC7L2;sp|Q9Y383-2|LC7L2_HUMAN Isoform 2 of Putative RNA-binding protei2,70Proteasome activator complex subunit 2 PSME2 tr|H0YM70|H0YM70_HUMAN Proteasome activator complex subunit 2 OS=Homo sapiens GN=PSME2 PE=2 SV=1;sp|Q9UL46|PSME2_HUMAN Proteasome activator complex subunit 2 OS=Homo sapiens GN=PSME2 PE=1 SV=42,69ATP-dependent DNA helicase Q4 RECQL4 tr|U3KQ17|U3KQ17_HUMAN ATP-dependent DNA helicase Q4 OS=Homo sapiens GN=RECQL4 PE=4 SV=1;sp|O94761|RECQ4_HUMAN ATP-dependent DNA helicase Q4 OS=Homo sapiens GN=RECQL4 PE=1 SV=1;tr|V9GYB6|V9GYB6_HUMAN ATP-dependent DNA helicase Q4 (Fragment) OS=Homo sapiens2,69Proteasome activator complex subunit 1 PSME1 tr|H0YNE3|H0YNE3_HUMAN Proteasome activator complex subunit 1 OS=Homo sapiens GN=PSME1 PE=2 SV=1;sp|Q06323|PSME1_HUMAN Proteasome activator complex subunit 1 OS=Homo sapiens GN=PSME1 PE=1 SV=1;sp|Q06323-2|PSME1_HUMAN Isoform 2 of Proteasome activator compl2,68

Page 39: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Merlin NF2 sp|P35240-4|MERL_HUMAN Isoform 4 of Merlin OS=Homo sapiens GN=NF2;sp|P35240-6|MERL_HUMAN Isoform 6 of Merlin OS=Homo sapiens GN=NF2;sp|P35240-5|MERL_HUMAN Isoform 5 of Merlin OS=Homo sapiens GN=NF2;sp|P35240-8|MERL_HUMAN Isoform 8 of Merlin OS=Homo sapiens2,68Branched-chain-amino-acid aminotransferase, cytosolicBCAT1 sp|P54687-2|BCAT1_HUMAN Isoform 2 of Branched-chain-amino-acid aminotransferase, cytosolic OS=Homo sapiens GN=BCAT1;sp|P54687-3|BCAT1_HUMAN Isoform 3 of Branched-chain-amino-acid aminotransferase, cytosolic OS=Homo sapiens GN=BCAT1;sp|P54687-4|BCAT1_HUMAN 2,68Heat shock protein HSP 90-beta HSP90AB1 sp|P08238|HS90B_HUMAN Heat shock protein HSP 90-beta OS=Homo sapiens GN=HSP90AB1 PE=1 SV=42,66Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform;Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoformPPP2R1A;PPP2R1Bsp|P30153|2AAA_HUMAN Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform OS=Homo sapiens GN=PPP2R1A PE=1 SV=4;tr|E9PPI5|E9PPI5_HUMAN Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform OS=Homo sapi2,64Tubulin alpha-1A chain;Tubulin alpha-1C chain;Tubulin alpha-1B chainTUBA1A;TUBA1C;TUBA1Bsp|Q71U36-2|TBA1A_HUMAN Isoform 2 of Tubulin alpha-1A chain OS=Homo sapiens GN=TUBA1A;sp|Q71U36|TBA1A_HUMAN Tubulin alpha-1A chain OS=Homo sapiens GN=TUBA1A PE=1 SV=1;tr|F5H5D3|F5H5D3_HUMAN Tubulin alpha-1C chain OS=Homo sapiens GN=TUBA1C PE=2 SV=1;sp|Q9BQ2,63Prolyl 3-hydroxylase 1 LEPRE1 sp|Q32P28|P3H1_HUMAN Prolyl 3-hydroxylase 1 OS=Homo sapiens GN=LEPRE1 PE=1 SV=2;sp|Q32P28-3|P3H1_HUMAN Isoform 3 of Prolyl 3-hydroxylase 1 OS=Homo sapiens GN=LEPRE1;tr|H7C0D1|H7C0D1_HUMAN Prolyl 3-hydroxylase 1 (Fragment) OS=Homo sapiens GN=LEPRE1 PE=4 SV=2,61SHC-transforming protein 1 SHC1 sp|P29353-5|SHC1_HUMAN Isoform 5 of SHC-transforming protein 1 OS=Homo sapiens GN=SHC1;sp|P29353-3|SHC1_HUMAN Isoform p46Shc of SHC-transforming protein 1 OS=Homo sapiens GN=SHC1;sp|P29353-2|SHC1_HUMAN Isoform p52Shc of SHC-transforming protein 1 OS=Homo s2,60Dihydropyrimidinase-related protein 2 DPYSL2 sp|Q16555-2|DPYL2_HUMAN Isoform 2 of Dihydropyrimidinase-related protein 2 OS=Homo sapiens GN=DPYSL2;sp|Q16555|DPYL2_HUMAN Dihydropyrimidinase-related protein 2 OS=Homo sapiens GN=DPYSL2 PE=1 SV=12,59Thyroid hormone receptor-associated protein 3THRAP3 sp|Q9Y2W1|TR150_HUMAN Thyroid hormone receptor-associated protein 3 OS=Homo sapiens GN=THRAP3 PE=1 SV=22,57Tubulin beta chain TUBB tr|Q5JP53|Q5JP53_HUMAN Tubulin beta chain OS=Homo sapiens GN=TUBB PE=2 SV=1;sp|P07437|TBB5_HUMAN Tubulin beta chain OS=Homo sapiens GN=TUBB PE=1 SV=2;tr|Q5ST81|Q5ST81_HUMAN Tubulin beta chain OS=Homo sapiens GN=TUBB PE=2 SV=1;tr|E9PBJ4|E9PBJ4_HUMAN Tubulin2,56Ubiquitin carboxyl-terminal hydrolase 5 USP5 sp|P45974-2|UBP5_HUMAN Isoform Short of Ubiquitin carboxyl-terminal hydrolase 5 OS=Homo sapiens GN=USP5;sp|P45974|UBP5_HUMAN Ubiquitin carboxyl-terminal hydrolase 5 OS=Homo sapiens GN=USP5 PE=1 SV=22,5614-3-3 protein zeta/delta YWHAZ tr|E7EX29|E7EX29_HUMAN 14-3-3 protein zeta/delta (Fragment) OS=Homo sapiens GN=YWHAZ PE=2 SV=1;sp|P63104|1433Z_HUMAN 14-3-3 protein zeta/delta OS=Homo sapiens GN=YWHAZ PE=1 SV=1;tr|E5RIR4|E5RIR4_HUMAN 14-3-3 protein zeta/delta (Fragment) OS=Homo sapiens GN2,55Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, gamma-enteric smooth muscle;Actin, aortic smooth muscleACTG1;ACTB;ACTA1;ACTC1;ACTG2;ACTA2sp|P63261|ACTG_HUMAN Actin, cytoplasmic 2 OS=Homo sapiens GN=ACTG1 PE=1 SV=1;sp|P60709|ACTB_HUMAN Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1;tr|I3L3I0|I3L3I0_HUMAN Actin, cytoplasmic 2, N-terminally processed (Fragment) OS=Homo sapiens GN=ACTG12,55Poly(rC)-binding protein 2;Poly(rC)-binding protein 3PCBP2;PCBP3 tr|H3BRU6|H3BRU6_HUMAN Poly(rC)-binding protein 2 (Fragment) OS=Homo sapiens GN=PCBP2 PE=4 SV=1;tr|F8VZX2|F8VZX2_HUMAN Poly(rC)-binding protein 2 OS=Homo sapiens GN=PCBP2 PE=2 SV=1;tr|G3V0E8|G3V0E8_HUMAN Poly(RC) binding protein 2, isoform CRA_f OS=Homo sa2,55ADP/ATP translocase 2;ADP/ATP translocase 2, N-terminally processed;ADP/ATP translocase 1SLC25A5;SLC25A4 sp|P05141|ADT2_HUMAN ADP/ATP translocase 2 OS=Homo sapiens GN=SLC25A5 PE=1 SV=7;sp|P12235|ADT1_HUMAN ADP/ATP translocase 1 OS=Homo sapiens GN=SLC25A4 PE=1 SV=42,53Major vault protein MVP sp|Q14764|MVP_HUMAN Major vault protein OS=Homo sapiens GN=MVP PE=1 SV=42,53Tumor susceptibility gene 101 protein TSG101 tr|F5H442|F5H442_HUMAN Tumor susceptibility gene 101 protein OS=Homo sapiens GN=TSG101 PE=2 SV=1;sp|Q99816|TS101_HUMAN Tumor susceptibility gene 101 protein OS=Homo sapiens GN=TSG101 PE=1 SV=2;sp|Q99816-2|TS101_HUMAN Isoform 2 of Tumor susceptibility gene 2,51La-related protein 7 LARP7 sp|Q4G0J3|LARP7_HUMAN La-related protein 7 OS=Homo sapiens GN=LARP7 PE=1 SV=1;sp|Q4G0J3-3|LARP7_HUMAN Isoform 3 of La-related protein 7 OS=Homo sapiens GN=LARP7;tr|H0YA82|H0YA82_HUMAN La-related protein 7 (Fragment) OS=Homo sapiens GN=LARP7 PE=4 SV=1;sp|Q42,51Fragile X mental retardation syndrome-related protein 2FXR2 sp|P51116|FXR2_HUMAN Fragile X mental retardation syndrome-related protein 2 OS=Homo sapiens GN=FXR2 PE=1 SV=22,48Peflin PEF1 sp|Q9UBV8|PEF1_HUMAN Peflin OS=Homo sapiens GN=PEF1 PE=1 SV=12,47Annexin A2;Annexin;Putative annexin A2-like proteinANXA2;ANXA2P2 sp|P07355|ANXA2_HUMAN Annexin A2 OS=Homo sapiens GN=ANXA2 PE=1 SV=2;sp|P07355-2|ANXA2_HUMAN Isoform 2 of Annexin A2 OS=Homo sapiens GN=ANXA2;tr|H0YN42|H0YN42_HUMAN Annexin (Fragment) OS=Homo sapiens GN=ANXA2 PE=2 SV=1;tr|H0YMD0|H0YMD0_HUMAN Annexin (Fragme2,46Replication factor C subunit 3 RFC3 sp|P40938-2|RFC3_HUMAN Isoform 2 of Replication factor C subunit 3 OS=Homo sapiens GN=RFC3;sp|P40938|RFC3_HUMAN Replication factor C subunit 3 OS=Homo sapiens GN=RFC3 PE=1 SV=22,45Nuclear pore complex protein Nup155 NUP155 tr|E9PF10|E9PF10_HUMAN Nuclear pore complex protein Nup155 OS=Homo sapiens GN=NUP155 PE=2 SV=1;sp|O75694-2|NU155_HUMAN Isoform 2 of Nuclear pore complex protein Nup155 OS=Homo sapiens GN=NUP155;sp|O75694|NU155_HUMAN Nuclear pore complex protein Nup155 OS=H2,44Tumor protein p73 TP73 sp|O15350-12|P73_HUMAN Isoform 11 of Tumor protein p73 OS=Homo sapiens GN=TP73;sp|O15350-4|P73_HUMAN Isoform Delta of Tumor protein p73 OS=Homo sapiens GN=TP73;sp|O15350-10|P73_HUMAN Isoform dN-Gamma of Tumor protein p73 OS=Homo sapiens GN=TP73;sp|O15350-92,43Signal transducer and activator of transcription;Signal transducer and activator of transcription 1-alpha/betaSTAT1 tr|E9PH66|E9PH66_HUMAN Signal transducer and activator of transcription 1-alpha/beta (Fragment) OS=Homo sapiens GN=STAT1 PE=2 SV=1;tr|E7ENM1|E7ENM1_HUMAN Signal transducer and activator of transcription 1-alpha/beta (Fragment) OS=Homo sapiens GN=STAT1 PE=22,41Splicing factor U2AF 35 kDa subunit U2AF1 sp|Q01081|U2AF1_HUMAN Splicing factor U2AF 35 kDa subunit OS=Homo sapiens GN=U2AF1 PE=1 SV=3;sp|Q01081-4|U2AF1_HUMAN Isoform 4 of Splicing factor U2AF 35 kDa subunit OS=Homo sapiens GN=U2AF1;sp|Q01081-2|U2AF1_HUMAN Isoform 2 of Splicing factor U2AF 35 kDa 2,35Melanoma-associated antigen D2 MAGED2 tr|Q5H907|Q5H907_HUMAN Melanoma antigen family D, 2, isoform CRA_d OS=Homo sapiens GN=MAGED2 PE=2 SV=1;tr|Q5H909|Q5H909_HUMAN Melanoma-associated antigen D2 OS=Homo sapiens GN=MAGED2 PE=2 SV=2;sp|Q9UNF1-2|MAGD2_HUMAN Isoform 2 of Melanoma-associated antige2,35Uncharacterized protein C3orf17 C3orf17 tr|E9PFF8|E9PFF8_HUMAN Uncharacterized protein C3orf17 OS=Homo sapiens GN=C3orf17 PE=2 SV=1;tr|A8MVI8|A8MVI8_HUMAN Chromosome 3 open reading frame 17, isoform CRA_c OS=Homo sapiens GN=C3orf17 PE=2 SV=1;sp|Q6NW34-2|CC017_HUMAN Isoform 2 of Uncharacterized p2,35Isoamyl acetate-hydrolyzing esterase 1 homologIAH1 tr|H7C5G1|H7C5G1_HUMAN Isoamyl acetate-hydrolyzing esterase 1 homolog (Fragment) OS=Homo sapiens GN=IAH1 PE=4 SV=1;tr|B4DMV3|B4DMV3_HUMAN HCG1685787, isoform CRA_b OS=Homo sapiens GN=IAH1 PE=2 SV=1;sp|Q2TAA2|IAH1_HUMAN Isoamyl acetate-hydrolyzing esterase 2,33Monofunctional C1-tetrahydrofolate synthase, mitochondrialMTHFD1L sp|Q6UB35|C1TM_HUMAN Monofunctional C1-tetrahydrofolate synthase, mitochondrial OS=Homo sapiens GN=MTHFD1L PE=1 SV=12,33F-actin-capping protein subunit alpha-2 CAPZA2 sp|P47755|CAZA2_HUMAN F-actin-capping protein subunit alpha-2 OS=Homo sapiens GN=CAPZA2 PE=1 SV=32,30Ubiquitin-like modifier-activating enzyme 6 UBA6 sp|A0AVT1-2|UBA6_HUMAN Isoform 2 of Ubiquitin-like modifier-activating enzyme 6 OS=Homo sapiens GN=UBA6;sp|A0AVT1|UBA6_HUMAN Ubiquitin-like modifier-activating enzyme 6 OS=Homo sapiens GN=UBA6 PE=1 SV=1;tr|H0Y8S8|H0Y8S8_HUMAN Ubiquitin-like modifier-activa2,25Filamin-A FLNA tr|Q5HY54|Q5HY54_HUMAN Filamin-A OS=Homo sapiens GN=FLNA PE=2 SV=1;sp|P21333-2|FLNA_HUMAN Isoform 2 of Filamin-A OS=Homo sapiens GN=FLNA;sp|P21333|FLNA_HUMAN Filamin-A OS=Homo sapiens GN=FLNA PE=1 SV=42,25Heat shock protein beta-1 HSPB1 sp|P04792|HSPB1_HUMAN Heat shock protein beta-1 OS=Homo sapiens GN=HSPB1 PE=1 SV=2;tr|F8WE04|F8WE04_HUMAN Heat shock protein beta-1 OS=Homo sapiens GN=HSPB1 PE=2 SV=12,23Scaffold attachment factor B1 SAFB sp|Q15424-2|SAFB1_HUMAN Isoform 2 of Scaffold attachment factor B1 OS=Homo sapiens GN=SAFB;sp|Q15424|SAFB1_HUMAN Scaffold attachment factor B1 OS=Homo sapiens GN=SAFB PE=1 SV=4;sp|Q15424-4|SAFB1_HUMAN Isoform 4 of Scaffold attachment factor B1 OS=Homo sapi2,23Dolichol-phosphate mannosyltransferase subunit 1DPM1 tr|E9PHH5|E9PHH5_HUMAN Dolichol-phosphate mannosyltransferase OS=Homo sapiens GN=DPM1 PE=2 SV=1;tr|Q5QPK2|Q5QPK2_HUMAN Dolichol-phosphate mannosyltransferase OS=Homo sapiens GN=DPM1 PE=2 SV=1;tr|H0Y368|H0Y368_HUMAN Dolichol-phosphate mannosyltransferase (F2,22Treacle protein TCOF1 tr|J3KQ96|J3KQ96_HUMAN Treacle protein (Fragment) OS=Homo sapiens GN=TCOF1 PE=2 SV=1;tr|E7ETY2|E7ETY2_HUMAN Treacle protein OS=Homo sapiens GN=TCOF1 PE=2 SV=1;tr|E9PHK9|E9PHK9_HUMAN Treacle protein OS=Homo sapiens GN=TCOF1 PE=2 SV=1;sp|Q13428-2|TCOF_HUMAN 2,22Palladin PALLD sp|Q8WX93-3|PALLD_HUMAN Isoform 3 of Palladin OS=Homo sapiens GN=PALLD;sp|Q8WX93|PALLD_HUMAN Palladin OS=Homo sapiens GN=PALLD PE=1 SV=3;sp|Q8WX93-8|PALLD_HUMAN Isoform 8 of Palladin OS=Homo sapiens GN=PALLD;sp|Q8WX93-5|PALLD_HUMAN Isoform 5 of Palladin OS2,21

UBBP4 tr|J3QLP7|J3QLP7_HUMAN Protein UBBP4 OS=Homo sapiens GN=UBBP4 PE=2 SV=1;tr|J3QRK5|J3QRK5_HUMAN Protein UBBP4 OS=Homo sapiens GN=UBBP4 PE=2 SV=1;tr|J3KSM4|J3KSM4_HUMAN Protein UBBP4 (Fragment) OS=Homo sapiens GN=UBBP4 PE=2 SV=12,21Thioredoxin-dependent peroxide reductase, mitochondrialPRDX3 tr|E9PH29|E9PH29_HUMAN Thioredoxin-dependent peroxide reductase, mitochondrial OS=Homo sapiens GN=PRDX3 PE=2 SV=1;sp|P30048|PRDX3_HUMAN Thioredoxin-dependent peroxide reductase, mitochondrial OS=Homo sapiens GN=PRDX3 PE=1 SV=32,20Clathrin heavy chain 1 CLTC sp|Q00610-2|CLH1_HUMAN Isoform 2 of Clathrin heavy chain 1 OS=Homo sapiens GN=CLTC;sp|Q00610|CLH1_HUMAN Clathrin heavy chain 1 OS=Homo sapiens GN=CLTC PE=1 SV=5;tr|J3KS13|J3KS13_HUMAN Clathrin heavy chain 1 OS=Homo sapiens GN=CLTC PE=2 SV=12,20Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolaseFASN sp|P49327|FAS_HUMAN Fatty acid synthase OS=Homo sapiens GN=FASN PE=1 SV=32,19Far upstream element-binding protein 2 KHSRP sp|Q92945|FUBP2_HUMAN Far upstream element-binding protein 2 OS=Homo sapiens GN=KHSRP PE=1 SV=4;tr|M0R0I5|M0R0I5_HUMAN Far upstream element-binding protein 2 (Fragment) OS=Homo sapiens GN=KHSRP PE=4 SV=12,19Cofilin-1 CFL1 sp|P23528|COF1_HUMAN Cofilin-1 OS=Homo sapiens GN=CFL1 PE=1 SV=3;tr|G3V1A4|G3V1A4_HUMAN Cofilin 1 (Non-muscle), isoform CRA_a OS=Homo sapiens GN=CFL1 PE=2 SV=1;tr|E9PP50|E9PP50_HUMAN Cofilin-1 (Fragment) OS=Homo sapiens GN=CFL1 PE=2 SV=1;tr|E9PK25|E9PK25_H2,18Galectin-1 LGALS1 sp|P09382|LEG1_HUMAN Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=22,18Charged multivesicular body protein 1a CHMP1A tr|F8VVT7|F8VVT7_HUMAN Charged multivesicular body protein 1a OS=Homo sapiens GN=CHMP1A PE=2 SV=1;sp|Q9HD42|CHM1A_HUMAN Charged multivesicular body protein 1a OS=Homo sapiens GN=CHMP1A PE=1 SV=1;tr|F8VUA2|F8VUA2_HUMAN Charged multivesicular body protein 1a2,17Transgelin-2 TAGLN2 sp|P37802|TAGL2_HUMAN Transgelin-2 OS=Homo sapiens GN=TAGLN2 PE=1 SV=32,16T-complex protein 1 subunit zeta-2 CCT6B sp|Q92526-2|TCPW_HUMAN Isoform 2 of T-complex protein 1 subunit zeta-2 OS=Homo sapiens GN=CCT6B;sp|Q92526-3|TCPW_HUMAN Isoform 3 of T-complex protein 1 subunit zeta-2 OS=Homo sapiens GN=CCT6B;sp|Q92526|TCPW_HUMAN T-complex protein 1 subunit zeta-2 OS=Homo 2,14Protein deglycase DJ-1 PARK7 tr|K7ELW0|K7ELW0_HUMAN Protein DJ-1 OS=Homo sapiens GN=PARK7 PE=2 SV=1;sp|Q99497|PARK7_HUMAN Protein DJ-1 OS=Homo sapiens GN=PARK7 PE=1 SV=2;tr|K7EN27|K7EN27_HUMAN Protein DJ-1 (Fragment) OS=Homo sapiens GN=PARK7 PE=2 SV=12,13LanC-like protein 2 LANCL2 sp|Q9NS86|LANC2_HUMAN LanC-like protein 2 OS=Homo sapiens GN=LANCL2 PE=1 SV=12,12Hematological and neurological expressed 1-like proteinHN1L tr|H3BMT0|H3BMT0_HUMAN Hematological and neurological-expressed 1-like protein (Fragment) OS=Homo sapiens GN=HN1L PE=2 SV=1;tr|H3BTV5|H3BTV5_HUMAN Hematological and neurological-expressed 1-like protein (Fragment) OS=Homo sapiens GN=HN1L PE=2 SV=1;tr|H3BU12,11Acyl-protein thioesterase 2 LYPLA2 tr|Q5QPQ0|Q5QPQ0_HUMAN Acyl-protein thioesterase 2 OS=Homo sapiens GN=LYPLA2 PE=2 SV=1;sp|O95372|LYPA2_HUMAN Acyl-protein thioesterase 2 OS=Homo sapiens GN=LYPLA2 PE=1 SV=1;tr|Q5QPQ1|Q5QPQ1_HUMAN Acyl-protein thioesterase 2 (Fragment) OS=Homo sapiens GN=LY2,09Mitotic checkpoint protein BUB3 BUB3 tr|B4DDM6|B4DDM6_HUMAN Mitotic checkpoint protein BUB3 OS=Homo sapiens GN=BUB3 PE=2 SV=1;tr|J3QT28|J3QT28_HUMAN Mitotic checkpoint protein BUB3 (Fragment) OS=Homo sapiens GN=BUB3 PE=2 SV=1;sp|O43684-2|BUB3_HUMAN Isoform 2 of Mitotic checkpoint protein BUB32,08Calpain small subunit 1;Calpain small subunit 2CAPNS1;CAPNS2 tr|U3KQE2|U3KQE2_HUMAN Calpain small subunit 1 (Fragment) OS=Homo sapiens GN=CAPNS1 PE=4 SV=1;tr|K7EIV0|K7EIV0_HUMAN Calpain small subunit 1 (Fragment) OS=Homo sapiens GN=CAPNS1 PE=2 SV=2;tr|K7ELJ7|K7ELJ7_HUMAN Calpain small subunit 1 OS=Homo sapiens GN=CA2,06Stromal membrane-associated protein 1 SMAP1 tr|E7ETU6|E7ETU6_HUMAN Stromal membrane-associated protein 1 OS=Homo sapiens GN=SMAP1 PE=2 SV=1;sp|Q8IYB5-3|SMAP1_HUMAN Isoform 3 of Stromal membrane-associated protein 1 OS=Homo sapiens GN=SMAP1;sp|Q8IYB5-2|SMAP1_HUMAN Isoform 2 of Stromal membrane-associ2,06Protein PRRC2B PRRC2B sp|Q5JSZ5-5|PRC2B_HUMAN Isoform 1 of Protein PRRC2B OS=Homo sapiens GN=PRRC2B;sp|Q5JSZ5|PRC2B_HUMAN Protein PRRC2B OS=Homo sapiens GN=PRRC2B PE=1 SV=22,05

Page 40: Supplemental Figure S1. DSB repair assays and generation ...genesdev.cshlp.org/content/suppl/2019/04/29/gad... · 4/29/2019  · (B) Schematic representation of the EJ5-GFP reporter

Protein RCC2 RCC2 sp|Q9P258|RCC2_HUMAN Protein RCC2 OS=Homo sapiens GN=RCC2 PE=1 SV=22,0414-3-3 protein theta YWHAQ sp|P27348|1433T_HUMAN 14-3-3 protein theta OS=Homo sapiens GN=YWHAQ PE=1 SV=1;tr|E9PG15|E9PG15_HUMAN 14-3-3 protein theta (Fragment) OS=Homo sapiens GN=YWHAQ PE=2 SV=12,04Rho guanine nucleotide exchange factor 2 ARHGEF2 tr|Q5VY93|Q5VY93_HUMAN Rho guanine nucleotide exchange factor 2 OS=Homo sapiens GN=ARHGEF2 PE=2 SV=1;tr|V9GYM8|V9GYM8_HUMAN Rho guanine nucleotide exchange factor 2 OS=Homo sapiens GN=ARHGEF2 PE=4 SV=1;sp|Q92974-3|ARHG2_HUMAN Isoform 3 of Rho guanine nucle2,04F-actin-capping protein subunit beta CAPZB tr|B1AK87|B1AK87_HUMAN Capping protein (Actin filament) muscle Z-line, beta, isoform CRA_a OS=Homo sapiens GN=CAPZB PE=2 SV=1;tr|B1AK88|B1AK88_HUMAN Capping protein (Actin filament) muscle Z-line, beta, isoform CRA_d OS=Homo sapiens GN=CAPZB PE=2 SV=1;sp|P2,04Tubulin beta-3 chain TUBB3 sp|Q13509|TBB3_HUMAN Tubulin beta-3 chain OS=Homo sapiens GN=TUBB3 PE=1 SV=2;tr|A8K854|A8K854_HUMAN HCG1983504, isoform CRA_f OS=Homo sapiens GN=TUBB3 PE=2 SV=12,03Src substrate cortactin CTTN sp|Q14247|SRC8_HUMAN Src substrate cortactin OS=Homo sapiens GN=CTTN PE=1 SV=2;sp|Q14247-3|SRC8_HUMAN Isoform 3 of Src substrate cortactin OS=Homo sapiens GN=CTTN;sp|Q14247-2|SRC8_HUMAN Isoform 2 of Src substrate cortactin OS=Homo sapiens GN=CTTN2,03Proline synthase co-transcribed bacterial homolog proteinPROSC sp|O94903|PROSC_HUMAN Proline synthase co-transcribed bacterial homolog protein OS=Homo sapiens GN=PROSC PE=1 SV=1;tr|E5RFX7|E5RFX7_HUMAN Proline synthase co-transcribed bacterial homolog protein (Fragment) OS=Homo sapiens GN=PROSC PE=2 SV=12,03Carbonyl reductase [NADPH] 1 CBR1 sp|P16152|CBR1_HUMAN Carbonyl reductase [NADPH] 1 OS=Homo sapiens GN=CBR1 PE=1 SV=3;tr|E9PQ63|E9PQ63_HUMAN Carbonyl reductase [NADPH] 1 OS=Homo sapiens GN=CBR1 PE=2 SV=1;tr|A8MTM1|A8MTM1_HUMAN Carbonyl reductase [NADPH] 1 OS=Homo sapiens GN=CBR1 PE=2 SV=1;2,01Fructose-2,6-bisphosphatase TIGAR TIGAR sp|Q9NQ88|TIGAR_HUMAN Fructose-2,6-bisphosphatase TIGAR OS=Homo sapiens GN=TIGAR PE=1 SV=12,01Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1GFPT1 sp|Q06210-2|GFPT1_HUMAN Isoform 2 of Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 OS=Homo sapiens GN=GFPT1;sp|Q06210|GFPT1_HUMAN Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 OS=Homo sapiens GN=GFPT1 PE=1 SV=32,00Kinesin-like protein;Kinesin-like protein KIF2CKIF2C tr|B7Z6Q6|B7Z6Q6_HUMAN Kinesin-like protein KIF2C OS=Homo sapiens GN=KIF2C PE=2 SV=1;sp|Q99661-2|KIF2C_HUMAN Isoform 2 of Kinesin-like protein KIF2C OS=Homo sapiens GN=KIF2C;sp|Q99661|KIF2C_HUMAN Kinesin-like protein KIF2C OS=Homo sapiens GN=KIF2C PE=1 SV=2,00