GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE71126 Query DataSets for GSE71126
Status Public on Mar 24, 2016
Title Sequence Features Accurately Predict Genome-wide MeCP2 Binding in vivo
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary MECP2 is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood. Using high-resolution MeCP2 binding data, we show that genetic features alone can predict binding with 88% accuracy. Integrating MeCP2 binding and DNA methylation in a probabilistic graphical model, we demonstrate that previously reported methylation preferences may be due to MeCP2’s affinity to GC-rich chromatin, a result replicated using published data. Furthermore, MeCP2 co-localized with nucleosomes, and Mecp2 deletion led to nucleosome repositioning. Finally, MeCP2 binding downstream of promoters correlated with increased expression in Mecp2 deficient neurons.
Overall design Study of genetic and epigenetic determinants of MeCP2 binding using MeCP2 ChIP-seq, MNase-seq, Bisulfite-seq and RNA-seq. Please see individual sample record for details on experimental design.
Contributor(s) Rube HT
Citation(s) 27008915
Submission date Jul 20, 2015
Last update date May 15, 2019
Contact name Hans Tomas Rube
Organization name University of Illinois at Urbana Champaign
Department Physics
Lab Jun Song
Street address 1110 West Green Street
City Urbana
State/province Illinois
ZIP/Postal code 61801
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (13)
GSM1827604 MeCP2_ChIP_WT_rep1
GSM1827605 MeCP2_ChIP_WT_rep2
GSM1827606 Input_WT_rep1
BioProject PRJNA290401
SRA SRP061339

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
GSE71126_RAW.tar 8.5 Gb (http)(custom) TAR (of BW, TSV)
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