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Series GSE19480 Query DataSets for GSE19480
Status Public on Feb 28, 2010
Title Understaning mechanisms underlying human gene expression variation with RNA sequencing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Understanding the genetic mechanisms underlying natural variation in gene expression is a central goal of both medical and evolutionary genetics, and studies of expression quantitative trait loci (eQTLs) have become an important tool for achieving this goal. While all eQTL studies to date have assayed mRNA levels using expression microarrays, recent advances in RNA sequencing enable the analysis of transcript variation at unprecedented resolution. We sequenced RNA from 69 lymphoblastoid cell lines (LCLs) derived from unrelated Nigerian individuals that have been extensively genotyped by the International HapMap Project. Pooling data from all individuals, we generated a map of the transcriptional landscape of these cells, identifying extensive use of unannotated polyadenylation sites and over 100 novel putative protein-coding exons. Using the genotypes from the HapMap project, we identified over a thousand genes at which genetic variation influences overall expression levels or splicing. We demonstrate that eQTLs near genes generally act via a mechanism involving allele-specific expression, and that variation that influences the inclusion of an exon is enriched within or near the consensus splice sites. Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing, and allele-specific expression across individuals.
Overall design RNA-Seq in 69 lymphoblastoid cell lines from multiple Yoruban HapMap individuals in at least two replicate lanes per individual
Contributor(s) Pickrell J, Pritchard J, Gilad Y
Citation(s) 20220758
Submission date Dec 15, 2009
Last update date May 15, 2019
Contact name Joseph Pickrell
Organization name University of Chicago
Street address 920 E. 58th St.
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (161)
GSM485364 NA19210_yale
GSM485365 NA19209_yale
GSM485366 NA19098_yale
SRA SRP001540
BioProject PRJNA122271

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Supplementary file Size Download File type/resource
GSE19480_RAW.tar 46.4 Gb (http)(custom) TAR (of MAP)
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Processed data provided as supplementary file
Raw data are available in SRA

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