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Series GSE12946 Query DataSets for GSE12946
Status Public on Oct 01, 2008
Title Alternative Isoform Regulation in Human Tissue Transcriptomes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of cDNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analysis of mappings of sequence reads to exon-exon junctions indicated that ~94% of human genes undergo alternative splicing (AS), ~86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that a majority of AS and alternative cleavage and polyadenylation (APA) events exhibit variation between tissues. Variations in alternative mRNA isoform expression between 6 individuals were also detected in cerebellar cortex, with ~2- to 3-fold less isoform variation observed between individuals than between tissues. Extreme or 'switch-like' regulation of splicing between tissues was associated with increased sequence conservation and with generation of full-length open reading frames. Patterns of AS and APA were strongly correlated across tissues, suggesting coordinated regulation, and sequence conservation of known regulatory motifs in both regulated introns and 3' UTRs suggested common involvement of the same factors in regulation of tissue-specific splicing and polyadenylation.
Overall design Exam mRNA expression in 15 human tissues and cell lines
Contributor(s) Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB
Citation(s) 18978772
Submission date Sep 26, 2008
Last update date May 15, 2019
Contact name Shujun Luo
Organization name Illumina inc
Street address 25861 Industrial Blvd
City Hayward
State/province CA
ZIP/Postal code 94545
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (16)
GSM325476 brain
GSM325477 liver
GSM325478 heart
SRA SRP000727
BioProject PRJNA110973

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Supplementary file Size Download File type/resource
GSE12946_RAW.tar 6.4 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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