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Series GSE20851 Query DataSets for GSE20851
Status Public on May 01, 2010
Title Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Contributor(s) Guttman M, Garber M, Lander E, Regev A
Citation(s) 20436462
Submission date Mar 12, 2010
Last update date May 15, 2019
Contact name Mitchell Guttman
E-mail(s) mguttman@mit.edu
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (3)
GSM521650 ESC_RNASeq
GSM521651 MLF_RNASeq
GSM521652 NPC_RNASeq
Relations
SRA SRP002325
BioProject PRJNA124759

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE20851_GSM521650_ES.aligned.sam.gz 5.9 Gb (ftp)(http) SAM
GSE20851_GSM521651_MLF.aligned.sam.gz 4.8 Gb (ftp)(http) SAM
GSE20851_GSM521652_NPC.aligned.sam.gz 3.9 Gb (ftp)(http) SAM
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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