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Series GSE131463 Query DataSets for GSE131463
Status Public on Jun 30, 2019
Title Nuclear speckles as a key regulator for the 3D genome organization [HiC]
Organism Mus musculus
Experiment type Other
Summary The nuclei of eukaryotes contain various higher-order chromatin architectures and nuclear bodies (NBs), which are critical for proper nuclear functions. By using mouse hepatocytes as the model, we knocked-down SRRM2, a core protein component scaffolding NSs, and performed Hi-C experiments to examine genome-wide chromatin interactions. We found that Srrm2 depletion disrupted the NSs and changes expression of about 1,000 genes. The intra-chromosomal interactions were decreased in type A (active) compartments and increased in type B (repressive) compartments. Furthermore, upon Srrm2 knockdown, the insulation of TADs was decreased specifically in active compartments, and the most significant reduction was found in the A1 sub-compartments. We showed that disruption of NSs by Srrm2 knockdown led to a global decrease of chromatin interactions in active compartments, indicating critical functions of NSs in the organization of the 3D genome.
Overall design HiC data in Control and SRRM2 KD AML12 cells.
Contributor(s) Hu SB, Lv P, Wen B
Citation(s) 31315647
Submission date May 20, 2019
Last update date Jul 29, 2019
Contact name Bo Wen
Organization name Fudan University
Department Institutes of Biomedical Sciences
Street address 130 DongAn Road
City Shanghai
ZIP/Postal code 200032
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (4)
GSM3780957 Aml12_Ctrl_rep1
GSM3780958 Aml12_Ctrl_rep2
GSM3780959 Aml12_KD_rep1
This SubSeries is part of SuperSeries:
GSE131466 Nuclear speckles as a key regulator for the 3D genome organization
BioProject PRJNA543774
SRA SRP198906

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE131463_RAW.tar 4.3 Gb (http)(custom) TAR (of HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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