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Series GSE66628 Query DataSets for GSE66628
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.
 
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)
GSM1626589 BMO_1 (exon)
GSM1626590 BMO_2 (exon)
GSM1626591 AGO_1 (exon)
This SubSeries is part of SuperSeries:
GSE66649 Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology
Relations
BioProject PRJNA277488

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE66628_RAW.tar 101.1 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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