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Series GSE30245 Query DataSets for GSE30245
Status Public on Aug 30, 2011
Title lincRNAs act in the circuitry controlling pluripotency and differentiation
Organism Mus musculus
Experiment type Expression profiling by array
Non-coding RNA profiling by array
Summary While thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem cells (ESC) and characterized the effects on gene expression. Here we show that knockdown of lincRNAs have major consequences on gene expression patterns, comparable to knockdown of well-known ESC regulators. Notably, lincRNAs primarily affect gene expression in trans. We identify dozens of lincRNAs whose knockdown causes an exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ESCs and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts physically bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ESC state.
 
Overall design We generated five lentiviral-based shRNAs targeting each of the 237 lincRNAs previously identified in ESCs. These shRNAs successfully targeted 147 lincRNAs and reduced their expression by an average of ~75% compared to endogenous levels in ESCs. As positive controls, we generated shRNAs targeting ~50 genes encoding regulatory proteins, including both transcription factor and chromatin factor genes that have been shown to play critical roles in ESC regulation; we obtained validated hairpins against 40 of these genes. As negative controls, we performed independent infections with lentiviruses containing 27 different shRNAs with no known cellular target RNA.
 
Contributor(s) Guttman M, Donaghey J, Lander E
Citation(s) 21874018
Submission date Jun 27, 2011
Last update date Jan 17, 2013
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)
GPL13767 Agilent Mouse 60K lincRNA Array
Samples (449)
GSM748909 ESC shRNA clonetechGfp_197_R1 (batch1)
GSM748910 ESC shRNA clonetechGfp_231_R1 (batch1)
GSM748911 ESC shRNA clonetechGfp_437_R1 (batch1)
Relations
BioProject PRJNA143775

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
GSE30245_RAW.tar 1.8 Gb (http)(custom) TAR (of TXT)
GSE30245_lincRNAHairpinSequences.txt.gz 70.6 Kb (ftp)(http) TXT
Processed data included within Sample table
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