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Series GSE44737 Query DataSets for GSE44737
Status Public on Oct 31, 2013
Title MBD3 localization by ChIP-seq
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS). Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression.
 
Overall design Identification of MBD3 localization in human breast cancer cell lines
 
Contributor(s) Shimbo T, Shi H, Wade PA, Du Y
Citation(s) 24385926
Submission date Feb 28, 2013
Last update date May 15, 2019
Contact name Takashi Shimbo
E-mail(s) shimbot@niehs.nih.gov
Organization name NIH/NIEHS
Street address 111 TW Alexander Dr.
City RTP
ZIP/Postal code 27709
Country USA
 
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (6)
GSM1089816 MCF-7_MBD3_input
GSM1089817 MCF-7_MBD3
GSM1089818 MDA231_MBD3_input
Relations
BioProject PRJNA191141
SRA SRP018926

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Supplementary file Size Download File type/resource
GSE44737_RAW.tar 1.3 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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