Mouse BIRN - Jagadeeswaran Rajendiran Pipeline Processing Environment.
Mouse BIRN CORE 4: Applications Mouse BIRN CORE 4: Applications.
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Transcript of Mouse BIRN CORE 4: Applications Mouse BIRN CORE 4: Applications.
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Mouse BIRNCORE 4: Applications
Mouse BIRNCORE 4: Applications
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1. Extend out from growing strengths in multi-modal multi-scale imaging of the mouse CNS to link up with numerous molecular and genetic resources. ADD LINKAGE to GENOMICS.
2. Provide a TRANSLATIONAL BRIDGE between mouse and human neurological disease that relies on common disease progression, shared behavior and phenotypes and MOLECULAR SIGNATURES.
3. VALIDATE models on two or more genetic backgrounds. What features are robust? What generalizes well between mouse and human populations?
1. Extend out from growing strengths in multi-modal multi-scale imaging of the mouse CNS to link up with numerous molecular and genetic resources. ADD LINKAGE to GENOMICS.
2. Provide a TRANSLATIONAL BRIDGE between mouse and human neurological disease that relies on common disease progression, shared behavior and phenotypes and MOLECULAR SIGNATURES.
3. VALIDATE models on two or more genetic backgrounds. What features are robust? What generalizes well between mouse and human populations?
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Three models of neurodegenerationThree models of neurodegenerationMultiple sclerosis (Voskuhl, MOG EAE model) Multiple sclerosis (Voskuhl, MOG EAE model)
Alzheimer’s disease (Jankowsky, Human Tg line) Alzheimer’s disease (Jankowsky, Human Tg line)
Parkinson’s disease (Masliah, Human Tg line) Parkinson’s disease (Masliah, Human Tg line)
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Three stages of progression + controlMales and femalesTwo fully sequenced strains (C57BL/6J and
DBA/2J)Three replicates (± 2)As many modalities as possible
Three stages of progression + controlMales and femalesTwo fully sequenced strains (C57BL/6J and
DBA/2J)Three replicates (± 2)As many modalities as possible
Diana PriceDiana Price
General Design
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New Modality: mRNA expression levelNew Modality: mRNA expression level
~40,000 transcript assays Often use a split design (histo<–>array)Lumping vs splitting (whole brain)Will generate modulated transcript sets
Then what?
~40,000 transcript assays Often use a split design (histo<–>array)Lumping vs splitting (whole brain)Will generate modulated transcript sets
Then what?
Analysis of signature lists
Mediation with WebQTL
Analysis of signature lists
Mediation with WebQTL
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Analysis of disease signature lists withAnalysis of disease signature lists with
What is the network connectivity of list members?
What are the mechanistic common denominators of lists?
Are there final common pathways?
How do we ensure high quality lists? (Partial answer: replicate on two genetic backgrounds)
What is the network connectivity of list members?
What are the mechanistic common denominators of lists?
Are there final common pathways?
How do we ensure high quality lists? (Partial answer: replicate on two genetic backgrounds)
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Genetic CorrelationsGenetic Correlations
with Ken Manlywith Ken Manly
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Group AVamp8Vamp5RapsnSyngr4Snap23Syt3Rnp24Sybl1Syt8Acv1Syt7Syt10Sycp1Syt5
Group AVamp8Vamp5RapsnSyngr4Snap23Syt3Rnp24Sybl1Syt8Acv1Syt7Syt10Sycp1Syt5
Group BSnpa91Synj2Sybl1Syt4Syt5VdpVti1bRnp24Vamp3Sec22l1Syn2Syn1VapaVamp1Syt11Vamp4Vamp1
Group BSnpa91Synj2Sybl1Syt4Syt5VdpVti1bRnp24Vamp3Sec22l1Syn2Syn1VapaVamp1Syt11Vamp4Vamp1
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The Two Strains: C57BL/6J and DBA/2JThe Two Strains: C57BL/6J and DBA/2J
First two inbred strains made at TJL
Very extensive phenotype and CNS data
Disease susceptibility well characterized
1.8 million defined SNPs Large RI set
First two inbred strains made at TJL
Very extensive phenotype and CNS data
Disease susceptibility well characterized
1.8 million defined SNPs Large RI set
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What are recombinant inbred strains (RI)What are recombinant inbred strains (RI)
C57BL/6J (B)C57BL/6J (B) DBA/2J (D)DBA/2J (D)
F1F1
20 generations
brother-sister
matings
20 generations
brother-sister
matings
BXD1BXD1 BXD2BXD2 BXD80BXD80+ … ++ … +
F2F2
BXD RIStrain setBXD RI
Strain set
fullyinbredfully
inbred
isogenicisogenic
hetero-geneoushetero-
geneous
Recombined chromosomes are
needed for mapping
Recombined chromosomes are
needed for mapping
femalefemale malemale
chromosome pairchromosome pair
InbredIsogenicsiblings
InbredIsogenicsiblings
BXDBXD
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Mediation with the MBL Mediation with the MBL
with Glenn Rosen
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Mouse Brain LibraryMouse Brain Library
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Low-res serial Nissl stain for stereologyLow-res serial Nissl stain for stereology
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Mediation with the iScopeMediation with the iScope
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Clique analysis: Mike Langston, Elissa Chesler
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CollaboratorsCollaborators
Ken ManlyJintao WangMichael LangstonMichele BaldwinGlenn Rosen
Ken ManlyJintao WangMichael LangstonMichele BaldwinGlenn Rosen
Lu Lu Elissa Chesler David Airey Jing Gu Shuhua Qi Hong Tao Zhang Arthur Centeno Yanhua Qu
Lu Lu Elissa Chesler David Airey Jing Gu Shuhua Qi Hong Tao Zhang Arthur Centeno Yanhua Qu
National Institute of Mental Health, National Institute on Drug Abuse, and the National Science Foundation (P20-MH 62009)
National Institute of Mental Health, National Institute on Drug Abuse, and the National Science Foundation (P20-MH 62009)