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SRX019275: GSM521650: ESC_RNASeq
3 ILLUMINA (Illumina Genome Analyzer II) runs: 58.1M spots, 8.8G bases, 5.8Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs
show Abstracthide Abstract
RNA-Seq provides an unbiased way to study a transcriptome, including both coding and non-coding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on studying expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply this approach to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known genes. We identify novel biological variation in protein-coding genes, including thousands of novel 5''-start sites, 3''-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to provide a comprehensive picture of mammalian transcriptomes. Overall design: RNA-Seq experiments of poly-A selected total RNA from embryonic stem cells, lung fibroblasts, and neural progenitor cells.
Sample: ESC_RNASeq
SAMN00011665 • SRS059567 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM521650: ESC_RNASeq
Instrument: Illumina Genome Analyzer II
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Spot descriptor:
forward77  reverse

Experiment attributes:
GEO Accession: GSM521650
Links:
External link:
Runs: 3 runs, 58.1M spots, 8.8G bases, 5.8Gb
Run# of Spots# of BasesSizePublished
SRR03999919,147,7012.9G1.9Gb2010-05-04
SRR04000019,756,5403G2Gb2010-05-04
SRR04000119,161,1542.9G1.9Gb2010-05-04

ID:
20693

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