|
|
GEO help: Mouse over screen elements for information. |
|
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) |
|
Relations |
SRA |
SRP002325 |
BioProject |
PRJNA124759 |
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 Selector |
Processed data are available on Series record |
Raw data are available in SRA |
|
|
|
|
|