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| Status |
Public on Sep 28, 2015 |
| Title |
Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology (Affymetrix_Gene1.0) (exon analysis) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
We present a more extensive and yet precise assessment to elucidate differences and similarities in performance at numerous aspects including signal range, sensitivity to fold-change, and fidelity with TaqMan qRT-PCR. There were three levels of data examined: entire data sets, data derived from gene name annotation oriented subset of 15442 RefSeq genes, and data derived from transcript pattern defined subset of 7034 RefSeq genes. Our results showed a fair degree of overall correlation between all 6 platforms evaluated; but, to varying degrees, two RNA-seq protocols outperformed three of the microarray platforms in most categories. Notably, a fourth microarray platform, Agilent, was comparable, or marginally superior, to the RNA-seq protocols within these same assessments. Furthermore, 3 platforms (Agilent and two RNA-seq methods) demonstrated over 80% concordance with the gold standard TaqMan assay in terms of fold-change accuracy. Our study suggests that the use of transcript patterns can enhance a number of the observed cross-platform correlations, indicating a potential usefulness for similar evaluations.
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| |
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| Overall design |
The study assessed differences and similarities in performance at numerous aspects including signal range, sensitivity to fold-change, and fidelity with TaqMan qRT-PCR. There were three levels of data examined: entire data sets, data derived from gene name annotation oriented subset of 15442 RefSeq genes, and data derived from transcript pattern defined subset of 7034 RefSeq genes.
|
| Web link |
http://www.biomedcentral.com/1471-2164/16/710
|
| |
|
| Contributor(s) |
Yu J, Head RD |
| Citation(s) |
26385698 |
| |
| Submission date |
Mar 06, 2015 |
| Last update date |
Jan 25, 2019 |
| Contact name |
Jinsheng Yu |
| E-mail(s) |
jyu@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Genetics
|
| Lab |
GTAC Lab
|
| Street address |
660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL6244 |
[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] |
| GPL10739 |
[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [probe set (exon) version] |
|
| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE66649 |
Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology |
|
| Relations |
| BioProject |
PRJNA277488 |
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