SpotQC Titration Experiment

SpotQC Titration Experiment

Eight different organism-specifc microarrays were hybridized with SpotQC at six different concentrations to determine the most ideal dilution to use for quality control.

Dilutions were as follows:

2 µM (SpotQC protocol)

1 µM

.5 µM

.25 µM

.1 µM

.01 µM


Tested 8 different organism print lots:

•QAF01122005A A. fumigatus

•QBA12012004A B. Anthracis

•QLM11222004A L. monocytogenes

•3QSA12292004A S. aureus

•QSM01042005A S. mutans

•2QSP11012004A S. pneumoniae

•QVC12032004A V. cholera

•QYP12102004A Y. pestis


Print plates for each print lot varied in age:

Date Created:

QAF01122005A 7/30/04

QBA12012004A 3/31/04

QLM11222004A 5/20/04

3QSA12292004A 12/22/04

QSM01042005A 4/8/04 (refreshed 12/3/04)

2QSP11012004A 4/8/04

QVC12032004A 3/11/04

QYP12102004A 3/11/04


Plates tested were 70mers or Amplicons:

QAF01122005A 70mer

QBA12012004A 70mer

QLM11222004A 70mer

3QSA12292004A 70mer

QSM01042005A 70mer

2QSP11012004A Amplicon

QVC12032004A 70mer

QYP12102004A 70mer


• Slides were hybridized according to SpotQC protocol.

• All slides were scanned on same scanner at PMT of 650.

• Spotfinder was used to generate data from each tif image.

• Log2 of signal intensities were calculated.

• Box plots of data were created using Origin 7.5.

• Data is visually represented as varying print lots across fixed concentrations as well as fixed print lots across varying concentrations.

QAF QBA QLM 3QSA QSM 2QSP QVC QYP

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Log2 Signal

0.01 Dilutions

QAF QBA QLM 3QSA QSM 2QSP QVC QYP 12

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Log2 Signal

0.1 uM DilutionQAF QBA QLM 3QSA QSM 2QSP QVC QYP

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Log2 Signal

0.25 uM Dilution


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Log2 Signal

0.5 uM DilutionQAF QBA QLM 3QSA QSM 2QSP QVC QYP

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Log2 Signal

1 uM Dilution


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Log2 Signal

2 uM Dilutions

Each chart below graphs the concentration of SpotQC across 8 different organism print lots.

QBA 2uM QBA 1uM QBA 0.5uM

QBA 0.25uM QBA 0.1QBA 0.01uM


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Log2 Signal

2 uM Dilutions


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Log2 Signal

1 uM Dilution


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Log2 Signal

0.5 uM Dilution


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Log2 Signal

0.25 uM Dilution


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Log2 Signal

0.1 uM Dilution


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Log2 Signal

0.01 Dilutions

2uM 1uM 0.5uM 0.25uM 0.1uM 0.01 uM12

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Log2 Signal

2QSP

2uM 1uM 0.5uM 0.25uM 0.1 uM 0.01uM12

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Log2 Signal

QSA2uM 1uM .5uM .25uM .1uM .01uM

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Log2 Signal

QBA

2uM 1uM .5uM .25uM .1uM .01 uM12

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Log2 Signal

QAF

2uM 1uM .5uM .25uM .1uM .01uM12

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Log2 Signal

QYP

2uM 1uM .5uM .25uM .1uM .01uM12

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Log2 Signal

QVC

2uM 1uM .5uM .25uM .1uM .01uM12

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Log2 Signal

QSM

2uM 1uM .5 Um .25uM .1 uM .01uM12

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Log2 Signal

QLM

Each chart below graphs an organism print lot at different SpotQC concentrations.

2uM 1uM .5uM .25uM .1uM .01 uM12

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Log2 Signal

QAF

2uM 1uM .5uM .25uM .1uM .01uM12

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Log2 Signal

QBA

2uM 1uM .5 Um .25uM .1 uM .01uM12

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Log2 Signal

QLM

2uM 1uM 0.5uM 0.25uM 0.1 uM 0.01uM12

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Log2 Signal

QSA

2uM 1uM .5uM .25uM .1uM .01uM12

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Log2 Signal

QSM

2uM 1uM 0.5uM 0.25uM 0.1uM 0.01 uM12

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Log2 Signal

2QSP

2uM 1uM .5uM .25uM .1uM .01uM12

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Log2 Signal

QVC

2uM 1uM .5uM .25uM .1uM .01uM12

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Log2 Signal

QYP

SpotQC Titration Experiment

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