GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE41006 Query DataSets for GSE41006
Status Public on Feb 08, 2013
Title Genome-wide identification of MBD2 and MBD3 binding sites by ChIP-seq
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The heterogeneous collection of NuRD complexes can be grouped into the MBD2 or MBD3 containing complexes MBD2-NuRD and MBD3-NuRD. Although functional differences have been described, a direct comparison of MBD2 and MBD3 in respect to genome-wide binding and function has been lacking. Here we show a strong enrichment for MBD2 at methylated CpG sequences, whereas CpGs bound by MBD3 are devoid of methylation. Gene activity of MBD2 bound genes is four fold lower as compared to genes bound by MBD3. When depleting cells for MBD2, the MBD2 bound genes increase their activity, whereas MBD2 plus MBD3 bound genes reduce their activity. Most strikingly, MBD3 is enriched at active promoters, whereas MBD2 is bound at methylated promoters and enriched at exon sequences of active genes. This suggests a functional connection between MBD2 binding to chromatin and splicing.
Overall design V5 ChIP followed by high throughput sequencing in HeLa cells transiently transfected with either V5-MBD2b, V5-MBD3 or V5.
Contributor(s) Guenther K, Renkawitz R, Bartkuhn M
Citation(s) 23361464
Submission date Sep 19, 2012
Last update date May 15, 2019
Contact name Marek Bartkuhn
Organization name Justus-Liebig-University Giessen
Department Biomedical Informatics and Systems Medicine
Street address Aulweg 132
City Giessen
State/province Hessen
ZIP/Postal code 35392
Country Germany
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (3)
GSM1006706 V5-HeLa_ChIP-Seq_control
GSM1006707 V5-MBD2-HeLa_ChIP-Seq
GSM1006708 V5-MBD3-HeLa_ChIP-Seq
This SubSeries is part of SuperSeries:
GSE41010 Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and exon sequences
BioProject PRJNA175530
SRA SRP015820

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
GSE41006_RAW.tar 713.4 Mb (http)(custom) TAR (of BED, TXT, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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