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Series GSE13765 Query DataSets for GSE13765
Status Public on Jan 01, 2009
Title lincRNA Expression
Organism Mus musculus
Experiment type Non-coding RNA profiling by genome tiling array
Expression profiling by array
Summary There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. While there are some well-characterized examples, the vast majority (>95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise. Here, we report a new approach to identifying large non-coding RNAs (ncRNAs) by using chromatin-state maps to discover discrete transcriptional units intervening known protein-coding loci. Our approach identified ~1600 large multi-exonic RNAs across four mouse cell types. In sharp contrast to previous collections, these large intervening ncRNAs (lincRNAs) exhibit strong purifying selection in their genomic loci, exonic sequences, and promoter regions – with greater than 95% showing clear evolutionary conservation. We also developed a novel functional genomics approach that assigns putative functions to each lincRNA, revealing a diverse range of roles for lincRNAs in processes from ES pluripotency to cell proliferation. We obtained independent functional validation for the predictions for over 100 lincRNAs, using cell-based assays. In particular, we demonstrate that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFKB, Sox2, Oc4, and Nanog. Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes.
 
Overall design lincRNA expression patterns were generated across a compendium of mouse tissues, cell types, and conditions.
lincRNA expression profiles were generated on custom NimbleGen arrays (Samples GSM346609..GSM346650) and correlated with known protein coding genes on Affymetrix gene expression arrays (Samples GSM347910..GSM347943).
 
Contributor(s) Guttman M, Rinn JL, Lander ES
Citation(s) 19182780
Submission date Nov 29, 2008
Last update date Feb 11, 2019
Contact name Mitchell Guttman
E-mail mguttman@mit.edu
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platforms (6)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
GPL7706 Mouse lincRNA Tiling Array (HD2 Platform)
GPL7707 Mouse lincRNA Tiling Array (HD1 Platform)
Samples (66)
GSM346609 Mouse Embryonic Fibroblasts (MEF) lincRNA Expression_rep1
GSM346610 Mouse Lung Fibroblasts (MLF) lincRNA Expression_rep1
GSM346611 Neural Precursor Cells (NPC) lincRNA Expression_rep1
Relations
BioProject PRJNA110767

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
GSE13765_RAW.tar 590.3 Mb (http)(custom) TAR (of CEL, GFF)
Raw data included within Sample table
Raw data provided as supplementary file
Processed data included within Sample table

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