Transcriptomics,Multiomics

Dataset Information

14

Understaning mechanisms underlying human gene expression variation with RNA sequencing


ABSTRACT: 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

OTHER RELATED OMICS DATASETS IN: PRJNA122271

ORGANISM(S): Homo sapiens  

SUBMITTER: Yoav Gilad   Joseph Pickrell  Jonathan Pritchard 

PROVIDER: E-GEOD-19480 | ArrayExpress | 2010-02-28

SECONDARY ACCESSION(S): SRP001540GSE19480PRJNA122271

REPOSITORIES: GEO, ArrayExpress, ENA

Dataset's files

Source:
Action DRS
E-GEOD-19480.idf.txt Idf
E-GEOD-19480.processed.1.zip Processed
E-GEOD-19480.processed.10.zip Processed
E-GEOD-19480.processed.100.zip Processed
E-GEOD-19480.processed.101.zip Processed
Items per page:
1 - 5 of 155
altmetric image

Publications


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. Although all eQTL studies so far have assayed messenger RNA levels using expression microarrays, recent advances in RNA sequencing enable the analysis of transcript variation at unprecedented resolution. We sequenced RNA from 69 lymphoblasto  ...[more]

Similar Datasets

2010-02-28 | E-GEOD-19480 | BioStudies
2010-02-28 | GSE19480 | GEO
2010-01-01 | S-EPMC3089435 | BioStudies
2009-01-01 | S-EPMC2766291 | BioStudies
2012-01-01 | S-EPMC3469421 | BioStudies
2014-01-01 | S-EPMC4028055 | BioStudies
2014-12-19 | E-GEOD-61742 | BioStudies
2011-01-01 | S-EPMC3134538 | BioStudies
2014-01-01 | S-EPMC3935516 | BioStudies
2007-01-01 | S-EPMC2683249 | BioStudies