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Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

Identifiers: SRA: SRP002325
BioProject: PRJNA124759
GEO: GSE20851
Study Type: 
Transcriptome Analysis
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.
Center Project: GSE20851
External Link: /pubmed:20436462

Related SRA data

Experiments:
4 ( 3 samples )
Runs:
7 (26.9Gbp; 14.1Gb)
Additional objects:
File type count
fastq 13