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E-GEOD-19480 - Understaning mechanisms underlying human gene expression variation with RNA sequencing

Status
Released on 28 February 2010, last updated on 24 May 2013
Organism
Homo sapiens
Samples (161)
Protocols (3)
Description
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. RNA-Seq in 69 lymphoblastoid cell lines from multiple Yoruban HapMap individuals in at least two replicate lanes per individual
Experiment type
RNA-seq of coding RNA 
Contacts
Joseph Pickrell <pickrell@uchicago.edu>, Jonathan Pritchard, Yoav Gilad
Citation
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. , PMID:20220758
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-19480.idf.txt
Sample and data relationshipE-GEOD-19480.sdrf.txt
Processed data (153)Click to browse processed data
Links