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Series GSE214123 Query DataSets for GSE214123
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 4]
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 Hi-C of K562 cells treated with PMA to differenitate into a megakaryocyte-like state after 0, 6, or 72h
 
Contributor(s) Bond ML, Quiroga IY, Love MI, Won H, Phanstiel DH
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Submission date Sep 24, 2022
Last update date Feb 07, 2023
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)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (42)
GSM6599326 HIC_K562_0000min_biorep1_techrep1_seqrep1
GSM6599327 HIC_K562_0360min_biorep1_techrep1_seqrep1
GSM6599328 HIC_K562_4320min_biorep1_techrep1_seqrep1
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 PRJNA883981

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
GSE214123_MEGA_K562_WT_0_inter.hic 5.2 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_360_inter.hic 6.2 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_4320_inter.hic 6.2 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_0_3_1_inter.hic 1.3 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_0_3_2_inter.hic 911.4 Mb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_0_4_1_inter.hic 1.2 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_0_4_2_inter.hic 1.2 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_360_3_1_inter.hic 1.4 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_360_3_2_inter.hic 1.0 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_360_4_1_inter.hic 1.2 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_360_4_2_inter.hic 1.3 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_4320_3_1_inter.hic 1.3 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_4320_3_2_inter.hic 1.3 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_4320_4_1_inter.hic 1.5 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_PMA_4320_4_2_inter.hic 1.4 Gb (ftp)(http) HIC
GSE214123_MEGA_K562_WT_inter.hic 23.4 Gb (ftp)(http) HIC
GSE214123_RAW.tar 19.7 Gb (http)(custom) TAR (of HIC)
GSE214123_hicSummary.txt.gz 1.8 Mb (ftp)(http) TXT
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Processed data provided as supplementary file
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