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| 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
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| 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.
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| Overall design |
Exam mRNA expression in 15 human tissues and cell lines
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| Contributor(s) |
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB |
| Citation(s) |
18978772 |
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| Submission date |
Sep 26, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Shujun Luo |
| E-mail(s) |
sluo@illumina.com
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| Organization name |
Illumina inc
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| Street address |
25861 Industrial Blvd
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| City |
Hayward |
| State/province |
CA |
| ZIP/Postal code |
94545 |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (16)
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| Relations |
| SRA |
SRP000727 |
| BioProject |
PRJNA110973 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12946_RAW.tar |
6.4 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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