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| Status |
Public on Sep 30, 2020 |
| Title |
Comparison of Affymetrix and NuGEN amplification methods for HTA 2.0 microarray |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Comparison of total RNA-seq and Affymetrix GeneChip(R) Human Transcriptome Array 2.0 analysis methods and Affymetrix GeneChip® WT PLUS Reagent and NuGEN Ovation® PICO WTA System V2 amplification methods for the detection of significant differentially expressed genes isolated from whole blood and brain RNA samples
Affymetrix and NuGEN amplification methods are compared to determine which is most efficient, cost effective, and accurate in the detection of differentialy expressed transcript clusters on the HTA 2.0 microarray
The optimum amplification microarray data is compared to total RNA-seq analysis of the same samples to determine which is the most efficient, cost effective, and accurate method of detecting differentially expressed genes
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| Overall design |
Samples containing 100% blood, 67% blood/33% brain, 33% blood/67% brain, and 100% brain -derived RNA were amplified and hybridized onto HTA 2.0 microarrays. In R, limma was used to test for differential expression. These same samples were analyzed using total RNA-seq and results were also analyzed for differential expression. A subset of overlapping microarray and RNA-seq genes were compared for differential expression and log fold change ranges. Counts of differentially expressed genes were also compared from complete microarray and RNA-seq datasets as well as log fold change ranges for both methodologies
Please note that Affymetrix and NuGEN datasets were normalized separately.
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| Web link |
https://www.faa.gov/data_research/research/med_humanfacs/oamtechreports/2020s/media/202009.pdf
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| Contributor(s) |
Munster SK, White VL, Hutchings DC, Burian DM, Nicholson SJ |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Sep 21, 2018 |
| Last update date |
Dec 30, 2020 |
| Contact name |
Susan Kasko Munster |
| E-mail(s) |
susan.munster@faa.gov
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| Organization name |
Federal Aviation Admininistration
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| Department |
Office of Aerospace Medicine
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| Lab |
Functional Genomics
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| Street address |
6500 S. MacArthur Blvd.
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| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73169 |
| Country |
USA |
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| Platforms (1) |
| GPL17586 |
[HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version] |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA492492 |
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