GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE140782 Query DataSets for GSE140782
Status Public on Aug 13, 2020
Title Highly connected enhancer communities control lineage-determining genes in human mesenchymal stem cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Adipocyte differentiation is driven by waves of transcriptional regulators that reprogram the en-hancer landscape and change the wiring of the promoter interactome. Here, we establish enhancer-capture Hi-C to interrogate the extent and role of enhancer-to-enhancer interactions during adi-pocyte differentiation of human mesenchymal stem cells. We find that enhancers form an elaborate network that is highly dynamic during differentiation and tightly coupled to changes of enhancer activity. These interactions are important for enhancer function, since transcription factors at baited enhancers stabilize transcription factor binding at target enhancers, a phenomenon we term cross-interaction stabilization of transcription factors (CIST). Moreover, highly interconnected enhancers (HICE) act as integration hubs orchestrating differentiation by formation of insulated 3D enhancer communities, inside which, HICE, and other enhancers, converge on phenotypically important gene promoters. Collectively, these results indicate that dynamic enhancer interactions play a key role in regulation of enhancer function, and that HICE are important for both signal integration and compartmentalization of the genome.
Overall design Genome-wide profiling of transcription factors using ChIP-seq, gene expression using RNA-seq and enhancer-anchored chromatin interactions using enhancer capture Hi-C during adipocyte differentiation of human mesenchymal stem cells.
Contributor(s) Madsen JG, Mandrup S
Citation(s) 33020665
Submission date Nov 21, 2019
Last update date Nov 16, 2020
Contact name Susanne Mandrup
Phone +45 6550 2340
Organization name University of Southern Denmark
Department Department of Biochemistry and Molecular Biologi
Street address Campusvej 55
City Odense M
State/province Fyn
ZIP/Postal code 5230
Country Denmark
Platforms (2)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (36)
GSM4340689 CEBPb ChIP-seq Msc Experiment #1
GSM4340690 CEBPb ChIP-seq Msc Experiment #2
GSM4340691 CEBPb ChIP-seq Adipocyte D1 Experiment #1
BioProject PRJNA590947
SRA SRP231151

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
GSE140782_CEBPb.CUTRUN.txt.gz 1.2 Mb (ftp)(http) TXT
GSE140782_CEBPb.ChIP.txt.gz 2.0 Mb (ftp)(http) TXT
GSE140782_CTCF.ChIP.txt.gz 1.6 Mb (ftp)(http) TXT
GSE140782_CUTRUN_CEBPb_Msc.counts.txt.gz 1.2 Mb (ftp)(http) TXT
GSE140782_CUTRUN_RUNX2_Msc.counts.txt.gz 1.2 Mb (ftp)(http) TXT
GSE140782_ChIP_CEBPb_Ad_D1.counts.txt.gz 1.6 Mb (ftp)(http) TXT
GSE140782_ChIP_CEBPb_Msc.counts.txt.gz 1.6 Mb (ftp)(http) TXT
GSE140782_ChIP_CTCF_Ad_D1.counts.txt.gz 1.6 Mb (ftp)(http) TXT
GSE140782_ChIP_CTCF_Msc.counts.txt.gz 1.6 Mb (ftp)(http) TXT
GSE140782_ChIP_MED1_Ad_D10.counts.txt.gz 1.5 Mb (ftp)(http) TXT
GSE140782_ChIP_RUNX2_Msc.counts.txt.gz 1.6 Mb (ftp)(http) TXT
GSE140782_ChIP_TEAD1_Ad_D1.counts.txt.gz 1.6 Mb (ftp)(http) TXT
GSE140782_ChIP_TEAD1_Msc.counts.txt.gz 1.6 Mb (ftp)(http) TXT
GSE140782_ChIP_TEAD4_Ad_D1.counts.txt.gz 1.5 Mb (ftp)(http) TXT
GSE140782_ChIP_TEAD4_Msc.counts.txt.gz 1.5 Mb (ftp)(http) TXT
GSE140782_ECHiC.txt.gz 49.7 Mb (ftp)(http) TXT
GSE140782_ECHiC_Adipogenesis.counts.txt.gz 49.8 Mb (ftp)(http) TXT
GSE140782_ECHiC_Lineages.counts.txt.gz 32.5 Mb (ftp)(http) TXT
GSE140782_HiC.bed.gz 29.4 Kb (ftp)(http) BED
GSE140782_HiC_Msc.bed.gz 29.3 Kb (ftp)(http) BED
GSE140782_MED1.ChIP.txt.gz 1.5 Mb (ftp)(http) TXT
GSE140782_RAW.tar 3.5 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
GSE140782_RNA.txt.gz 523.6 Kb (ftp)(http) TXT
GSE140782_RNA_Ad_D10.counts.txt.gz 523.9 Kb (ftp)(http) TXT
GSE140782_RUNX2.CUTRUN.txt.gz 1.2 Mb (ftp)(http) TXT
GSE140782_TEAD4.ChIP.txt.gz 1.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap