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
SpotQC Titration Experiment
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
SpotQC Titration Experiment
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
SpotQC Titration Experiment
Plates tested were 70mers or Amplicons:
QAF01122005A 70mer
QBA12012004A 70mer
QLM11222004A 70mer
3QSA12292004A 70mer
QSM01042005A 70mer
2QSP11012004A Amplicon
QVC12032004A 70mer
QYP12102004A 70mer
SpotQC Titration Experiment
• 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
12
14
16
18
20
22
24
Log2 Signal
0.01 Dilutions
QAF QBA QLM 3QSA QSM 2QSP QVC QYP 12
14
16
18
20
22
24
Log2 Signal
0.1 uM DilutionQAF QBA QLM 3QSA QSM 2QSP QVC QYP
12
14
16
18
20
22
24
Log2 Signal
0.25 uM Dilution
QAF QBA QLM 3QSA QSM 2QSP QVC QYP 12
14
16
18
20
22
24
Log2 Signal
0.5 uM DilutionQAF QBA QLM 3QSA QSM 2QSP QVC QYP
12
14
16
18
20
22
24
Log2 Signal
1 uM Dilution
QAF QBA QLM 3QSA QSM 2QSP QVC QYP 12
14
16
18
20
22
24
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
QAF QBA QLM 3QSA QSM 2QSP QVC QYP 12
14
16
18
20
22
24
Log2 Signal
2 uM Dilutions
QAF QBA QLM 3QSA QSM 2QSP QVC QYP 12
14
16
18
20
22
24
Log2 Signal
1 uM Dilution
QAF QBA QLM 3QSA QSM 2QSP QVC QYP 12
14
16
18
20
22
24
Log2 Signal
0.5 uM Dilution
QAF QBA QLM 3QSA QSM 2QSP QVC QYP
12
14
16
18
20
22
24
Log2 Signal
0.25 uM Dilution
QAF QBA QLM 3QSA QSM 2QSP QVC QYP
12
14
16
18
20
22
24
Log2 Signal
0.1 uM Dilution
QAF QBA QLM 3QSA QSM 2QSP QVC QYP 12
14
16
18
20
22
24
Log2 Signal
0.01 Dilutions
2uM 1uM 0.5uM 0.25uM 0.1uM 0.01 uM12
14
16
18
20
22
24
Log2 Signal
2QSP
2uM 1uM 0.5uM 0.25uM 0.1 uM 0.01uM12
14
16
18
20
22
24
Log2 Signal
QSA2uM 1uM .5uM .25uM .1uM .01uM
12
14
16
18
20
22
24
Log2 Signal
QBA
2uM 1uM .5uM .25uM .1uM .01 uM12
14
16
18
20
22
24
Log2 Signal
QAF
2uM 1uM .5uM .25uM .1uM .01uM12
14
16
18
20
22
24
Log2 Signal
QYP
2uM 1uM .5uM .25uM .1uM .01uM12
14
16
18
20
22
24
Log2 Signal
QVC
2uM 1uM .5uM .25uM .1uM .01uM12
14
16
18
20
22
24
Log2 Signal
QSM
2uM 1uM .5 Um .25uM .1 uM .01uM12
14
16
18
20
22
24
Log2 Signal
QLM
Each chart below graphs an organism print lot at different SpotQC concentrations.
2uM 1uM .5uM .25uM .1uM .01 uM12
14
16
18
20
22
24
Log2 Signal
QAF
2uM 1uM .5uM .25uM .1uM .01uM12
14
16
18
20
22
24
Log2 Signal
QBA
2uM 1uM .5 Um .25uM .1 uM .01uM12
14
16
18
20
22
24
Log2 Signal
QLM
2uM 1uM 0.5uM 0.25uM 0.1 uM 0.01uM12
14
16
18
20
22
24
Log2 Signal
QSA
2uM 1uM .5uM .25uM .1uM .01uM12
14
16
18
20
22
24
Log2 Signal
QSM
2uM 1uM 0.5uM 0.25uM 0.1uM 0.01 uM12
14
16
18
20
22
24
Log2 Signal
2QSP
2uM 1uM .5uM .25uM .1uM .01uM12
14
16
18
20
22
24
Log2 Signal
QVC
2uM 1uM .5uM .25uM .1uM .01uM12
14
16
18
20
22
24
Log2 Signal
QYP