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Series GSE163729 Query DataSets for GSE163729
Status Public on Feb 09, 2022
Title BRD2 regulates accessible genome organization
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary To dissect Cohesin-independent mechanisms that compartmentalize the mammalian genome, we combined super-resolution imaging and high-resolution chromatin interactome, chromatin binding and accessibility and RNA sequencing analysis. We found that the bromodomain and extra-terminal domain (BET) family protein BRD2 is one key regulator to promote compartmental interactions in the absence of Cohesin. We also identified competitive, rather than cooperative relationship between BET family proteins in shaping the 3D genome organization. This study uncovers new mechanisitc insights on the 3D organization of the mammalian genome.
 
Overall design We generated inducible protein degradation system for Cohesin subunit RAD21, BET family proteins in mouse embryonic stem cells (ESCs). We performed Micro-C, ChIP-seq, ATAC-seq and RNA-seq experiments and analysis after acute depleting individual protein or in combination.
 
Contributor(s) Xie L
Citation(s) 35410381
Submission date Dec 22, 2020
Last update date May 03, 2022
Contact name Robert Tjian
E-mail(s) jmlim@berkeley.edu
Organization name UC Berkeley/HHMI
Street address LKS
City Berkeley
State/province CA
ZIP/Postal code 94704
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21626 NextSeq 550 (Mus musculus)
Samples (97)
GSM4984742 Control B2 Micro-C
GSM4984743 Rad21 dep B2 Micro-C
GSM4984744 Brd2 dep Micro-C
Relations
BioProject PRJNA687275
SRA SRP298987

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
GSE163729_RAW.tar 22.9 Gb (http)(custom) TAR (of BW, HIC, MCOOL)
GSE163729_Table_S1_Differential_expressed_genes_BRD2_depletion_6h.xlsx 25.4 Kb (ftp)(http) XLSX
GSE163729_Table_S2_Differential_expressed_genes_BRD4_depletion_6h.xlsx 186.8 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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