NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE31486 Query DataSets for GSE31486
Status Public on Oct 06, 2011
Title CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons.
 
Overall design CTCF ChIP-seq was performed in BJAB and BL41 B cell lines and normalized relative to Rabbit Ig control IP-seq reads. RNA-seq was performed in BJAB and BL41 cells transduced with shRNA against CTCF or RFP as a control, and in untransduced cells as well.
 
Contributor(s) Shukla S, Oberdoerffer S, Sandberg R
Citation(s) 21964334
Submission date Aug 18, 2011
Last update date May 15, 2019
Contact name Shalini Oberdoerffer
E-mail(s) shalini.oberdoerffer@nih.gov
Phone 301-846-7104
Organization name National Cancer Institute
Street address 1050 Boyles Street
City Frederick
State/province MD
ZIP/Postal code 21702
Country USA
 
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (6)
GSM782160 BJAB
GSM782161 BJAB_shRFP
GSM782162 BJAB_shCTCF
This SubSeries is part of SuperSeries:
GSE31278 CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing
Relations
SRA SRP007885
BioProject PRJNA154053

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
GSE31486_inclusionlevels.txt.gz 853.6 Kb (ftp)(http) TXT
GSE31486_inclusionlevels_description.txt.gz 544 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap