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Series GSE102997 Query DataSets for GSE102997
Status Public on May 11, 2018
Title CTCF and Cohesin (Rad21) ChIP-seq in male mouse liver
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study where we describe features of Topologically Associating Domains (TADs) and their impact on liver gene expression, then use these features to computationally predict subTAD structures not otherwise readily identifiable due to the low resolution of Hi-C. Our findings reveal that CTCF-based subTAD loops maintain key insulating properties of TADs, and support the proposal that subTADs are formed by the same loop extrusion mechanism and contribute to nuclear architecture as intra-TAD scaffolds that further constrain enhancer-promoter interactions. This allows high expression of super enhancer target genes and individual genes within inactive TADs, and may be a broadly conserved mechanism of genomic regulation.
Overall design CTCF and Cohesin (Rad21) ChIP-seq in mouse liver
Contributor(s) Matthews BJ, Shin A, Waxman DJ
Citation(s) 29757144, 32680543
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 DK033765 Regulation of Sex Differences in Liver Metabolism BOSTON UNIVERSITY CHARLES RIVER CAMPUS DAVID J WAXMAN
R01 ES024421 Epigenetic Actions of Environmental Chemicals BOSTON UNIVERSITY CHARLES RIVER CAMPUS DAVID J WAXMAN
Submission date Aug 23, 2017
Last update date Jul 27, 2020
Contact name David J. Waxman
Organization name Boston University
Department Department of Biology and Bioinformatics Program
Street address 5 Cummington Mall
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (7)
GSM2752307 Male_Rad21chip_Repl1_G133_M3
GSM2752308 Male_Rad21chip_Repl2_G133_M6
GSM2752309 Male_Rad21chip_Repl3_G100_M5
This SubSeries is part of SuperSeries:
GSE102999 Computational prediction of CTCF/cohesin-based intra-TAD (sbTAD) loops that insulate chromatin contacts and gene expression in mouse liver
BioProject PRJNA399718
SRA SRP116021

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
GSE102997_CTCF_category.bed.gz 777.4 Kb (ftp)(http) BED
GSE102997_Male_CTCF_merged.bed.gz 2.0 Mb (ftp)(http) BED
GSE102997_Male_Rad21_merged.bed.gz 1.8 Mb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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