NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE213908 Query DataSets for GSE213908
Status Public on Nov 01, 2022
Title Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features [dataset 3]
Organism Homo sapiens
Experiment type Other
Summary 3D chromatin structure is thought to play a critical role in regulating gene transcription during cellular transitions. While our understanding of loop formation and maintenance is rapidly improving, much less is known about the mechanisms driving changes in looping and the impact of differential looping on gene transcription. One limitation has been a lack of well powered differential looping data sets. To address this, we conducted a deeply sequenced Hi-C time course of megakaryocyte development comprising 4 biological replicates and 6 billion reads per time point. Statistical analysis revealed 1,503 differential loops. Gained loops were enriched for AP-1 occupancy and correlated with increased expression of genes at their anchors. Lost loops were characterized by increases in expression of genes within the loop boundaries. Linear modeling revealed that changes in histone H3K27 acetylation, chromatin accessibility, and JUN binding in between the loop anchors were often just as predictive of changes in loop strength as changes to CTCF and/or cohesin occupancy at loop anchors. Finally, we built linear models and found that incorporating the dynamics of enhancer acetylation and loop strength increased accuracy of gene expression predictions. Together, our well-powered study has added to our understanding of the mechanisms that regulate looping, and the relationship of looping with gene expression.
 
Overall design RNA-seq of K562 cells treated with PMA to differenitate into a megakaryocyte-like state after 0, 0.5, 1.5, 3, 6, 24, 48, or 72h
 
Contributor(s) Bond ML, Quiroga IY, Love MI, Won H, Phanstiel DH
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Sep 21, 2022
Last update date Nov 03, 2022
Contact name Marielle Bond
E-mail(s) marielle@live.unc.edu
Phone 7044913933
Organization name UNC Chapel Hill
Department Genetics Curriculum
Lab Phanstiel
Street address 104 Manning Drive Thurston Building Room 4012
City Chapel Hill
State/province North Carolina
ZIP/Postal code 27599
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (22)
GSM6596367 CNR_K562_0000min_H3K27ac_rep1
GSM6596368 CNR_K562_0360min_H3K27ac_rep1
GSM6596369 CNR_K562_4320min_H3K27ac_rep1
This SubSeries is part of SuperSeries:
GSE213909 Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features
Relations
BioProject PRJNA882942

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
GSE213908_CTCFSummary.txt.gz 3.0 Mb (ftp)(http) TXT
GSE213908_H3K27Summary.txt.gz 4.7 Mb (ftp)(http) TXT
GSE213908_JunSummary.txt.gz 6.6 Mb (ftp)(http) TXT
GSE213908_MERGE_MEGA_ChIP_CTCF_K562_WT_PMA_0_S.bw 163.1 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_CTCF_K562_WT_PMA_360_S.bw 174.7 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_CTCF_K562_WT_PMA_4320_S.bw 199.1 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_H3K27_K562_WT_PMA_0_S.bw 116.4 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_H3K27_K562_WT_PMA_360_S.bw 142.9 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_H3K27_K562_WT_PMA_4320_S.bw 123.4 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_Jun_K562_WT_PMA_0_S.bw 200.3 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_Jun_K562_WT_PMA_360_S.bw 177.0 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_Jun_K562_WT_PMA_4320_S.bw 195.7 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_Rad21_K562_WT_PMA_0_S.bw 224.0 Mb (ftp)(http) BW
GSE213908_MERGE_MEGA_ChIP_Rad21_K562_WT_PMA_4320_S.bw 233.3 Mb (ftp)(http) BW
GSE213908_RAW.tar 2.7 Gb (http)(custom) TAR (of BW, NARROWPEAK)
GSE213908_Rad21Summary.txt.gz 3.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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