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Series GSE85977 Query DataSets for GSE85977
Status Public on Aug 31, 2017
Title High-resolution Comparative Analysis Reveals a Primitive 3D Genome in Embryonic Stem Cells
Organism Homo sapiens
Experiment type Other
Third-party reanalysis
Summary The landscape of human epigenome undergoes extensive changes during development, leading to distinct transcription programs in different cell types. It is however still not clear how the high-order genome organization reshapes in cellular differentiation. Using Hi-C, we compared the comprehensive 3D genome maps in human embryonic stem cells (ESCs) and two differentiated cell types at kilobase resolution. Consistent with previous reports, we found that the CTCF protein anchors long-range constitutive interactions that are invariant between different cell types. The most stable DNA contacts in ESC are between a few hundred genomic loci with strongest histone H3 lysine 27 tri-methylation (H3K27me3) binding, which plays a key role maintaining pluripotency by inhibiting key development genes. These repressive 3D chromatin structures are resolved in differentiated cells, accompanied by redistribution of H3K27me3 mark. Most surprisingly, we found that in human ESCs, DNA looping interactions are not enriched at enhancers, suggesting a stochastic nature of DNA looping interactions at ESC enhancers. This is in sharp contrast to differentiated cells, in which a majority of cell type specific DNA looping interactions are at enhancers, regardless of whether the enhancers are co-occupied by CTCF. Taken together, our analysis revealed a primitive enhancer-independent genome architecture in ESCs, which is consistent with the stem cell pluripotency and differentiation plasticity. Most of the stable DNA looping interactions associated with lineage-governing enhancers are created only during cell fate commitment.
 
Overall design We performed kilobase-resolution Hi-C analysis at fragment level in H1 hESCs, IMR90 and GM12878 cells. Identified DNA looping interactions are compared to chromatin marks in these cell types.
 
Contributor(s) Liu X, Li Y, Jin F
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Aug 24, 2016
Last update date May 15, 2019
Contact name Fulai Jin
E-mail(s) fxj45@case.edu
Phone 2163681811
Organization name Case Western Reserve University
Lab Fulai Jin
Street address 10900 Euclid Avenue
City Cleveland
State/province OH - OHIO
ZIP/Postal code 44106
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (4)
GSM2290058 Hi-C H1 replicate 3
GSM2290059 Hi-C H1 replicate 4
GSM2290060 Hi-C H1 replicate 5
Relations
Reanalysis of GSM1267196
Reanalysis of GSM1267197
Reanalysis of GSM1055800
Reanalysis of GSM1055801
Reanalysis of GSM1154021
Reanalysis of GSM1154022
Reanalysis of GSM1154023
Reanalysis of GSM1154024
Reanalysis of GSM1055802
Reanalysis of GSM1055803
Reanalysis of GSM1154025
Reanalysis of GSM1154026
Reanalysis of GSM1154027
Reanalysis of GSM1154028
Reanalysis of GSM1181867
Reanalysis of GSM1181868
Reanalysis of GSM1551583
Reanalysis of GSM1551584
Reanalysis of GSM1551586
Reanalysis of GSM1608505
BioProject PRJNA339933

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
GSE85977_GM12878.rep1.loop.inward.txt.gz 125.5 Mb (ftp)(http) TXT
GSE85977_GM12878.rep1.loop.outward.txt.gz 125.4 Mb (ftp)(http) TXT
GSE85977_GM12878.rep1.loop.samestrand.txt.gz 231.6 Mb (ftp)(http) TXT
GSE85977_GM12878.rep2.loop.inward.txt.gz 114.7 Mb (ftp)(http) TXT
GSE85977_GM12878.rep2.loop.outward.txt.gz 114.4 Mb (ftp)(http) TXT
GSE85977_GM12878.rep2.loop.samestrand.txt.gz 211.4 Mb (ftp)(http) TXT
GSE85977_GM12878.rep3.loop.inward.txt.gz 469.9 Mb (ftp)(http) TXT
GSE85977_GM12878.rep3.loop.outward.txt.gz 465.2 Mb (ftp)(http) TXT
GSE85977_GM12878.rep3.loop.samestrand.txt.gz 864.3 Mb (ftp)(http) TXT
GSE85977_GM12878.rep4.loop.inward.txt.gz 185.9 Mb (ftp)(http) TXT
GSE85977_GM12878.rep4.loop.outward.txt.gz 180.2 Mb (ftp)(http) TXT
GSE85977_GM12878.rep4.loop.samestrand.txt.gz 339.0 Mb (ftp)(http) TXT
GSE85977_GM12878.rep5.loop.inward.txt.gz 373.3 Mb (ftp)(http) TXT
GSE85977_GM12878.rep5.loop.outward.txt.gz 368.3 Mb (ftp)(http) TXT
GSE85977_GM12878.rep5.loop.samestrand.txt.gz 679.7 Mb (ftp)(http) TXT
GSE85977_GM12878.rep6.loop.inward.txt.gz 624.0 Mb (ftp)(http) TXT
GSE85977_GM12878.rep6.loop.outward.txt.gz 617.9 Mb (ftp)(http) TXT
GSE85977_GM12878.rep6.loop.samestrand.txt.gz 1.1 Gb (ftp)(http) TXT
GSE85977_H1.rep1.loop.inward.txt.gz 169.4 Mb (ftp)(http) TXT
GSE85977_H1.rep1.loop.outward.txt.gz 162.7 Mb (ftp)(http) TXT
GSE85977_H1.rep1.loop.samestrand.txt.gz 302.7 Mb (ftp)(http) TXT
GSE85977_H1.rep2.loop.inward.txt.gz 253.4 Mb (ftp)(http) TXT
GSE85977_H1.rep2.loop.outward.txt.gz 247.9 Mb (ftp)(http) TXT
GSE85977_H1.rep2.loop.samestrand.txt.gz 458.6 Mb (ftp)(http) TXT
GSE85977_HiC_stat.3_cells.within_2Mb.txt.gz 16.9 Gb (ftp)(http) TXT
GSE85977_IMR90.rep1.loop.inward.txt.gz 104.0 Mb (ftp)(http) TXT
GSE85977_IMR90.rep1.loop.outward.txt.gz 98.2 Mb (ftp)(http) TXT
GSE85977_IMR90.rep1.loop.samestrand.txt.gz 187.1 Mb (ftp)(http) TXT
GSE85977_IMR90.rep2.loop.inward.txt.gz 122.5 Mb (ftp)(http) TXT
GSE85977_IMR90.rep2.loop.outward.txt.gz 119.1 Mb (ftp)(http) TXT
GSE85977_IMR90.rep2.loop.samestrand.txt.gz 226.1 Mb (ftp)(http) TXT
GSE85977_IMR90.rep3.loop.inward.txt.gz 57.2 Mb (ftp)(http) TXT
GSE85977_IMR90.rep3.loop.outward.txt.gz 52.9 Mb (ftp)(http) TXT
GSE85977_IMR90.rep3.loop.samestrand.txt.gz 99.5 Mb (ftp)(http) TXT
GSE85977_IMR90.rep4.loop.inward.txt.gz 47.8 Mb (ftp)(http) TXT
GSE85977_IMR90.rep4.loop.outward.txt.gz 43.5 Mb (ftp)(http) TXT
GSE85977_IMR90.rep4.loop.samestrand.txt.gz 81.7 Mb (ftp)(http) TXT
GSE85977_IMR90.rep5.loop.inward.txt.gz 44.1 Mb (ftp)(http) TXT
GSE85977_IMR90.rep5.loop.outward.txt.gz 39.4 Mb (ftp)(http) TXT
GSE85977_IMR90.rep5.loop.samestrand.txt.gz 74.2 Mb (ftp)(http) TXT
GSE85977_IMR90.rep6.loop.inward.txt.gz 42.8 Mb (ftp)(http) TXT
GSE85977_IMR90.rep6.loop.outward.txt.gz 39.2 Mb (ftp)(http) TXT
GSE85977_IMR90.rep6.loop.samestrand.txt.gz 73.9 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep1.loop.inward.txt.gz 115.4 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep1.loop.outward.txt.gz 114.3 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep1.loop.samestrand.txt.gz 212.9 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep2.loop.inward.txt.gz 204.3 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep2.loop.outward.txt.gz 200.5 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep2.loop.samestrand.txt.gz 376.0 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep3.loop.inward.txt.gz 65.7 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep3.loop.outward.txt.gz 62.6 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep3.loop.samestrand.txt.gz 118.9 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep4.loop.inward.txt.gz 87.1 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep4.loop.outward.txt.gz 82.8 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep4.loop.samestrand.txt.gz 157.7 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep5.loop.inward.txt.gz 29.8 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep5.loop.outward.txt.gz 26.8 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep5.loop.samestrand.txt.gz 50.3 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep6.loop.inward.txt.gz 59.9 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep6.loop.outward.txt.gz 56.1 Mb (ftp)(http) TXT
GSE85977_IMR90_TNF.rep6.loop.samestrand.txt.gz 106.7 Mb (ftp)(http) TXT
GSE85977_RAW.tar 687.4 Mb (http)(custom) TAR (of TXT)
GSE85977_anchors_2kb.bed.gz 4.7 Mb (ftp)(http) BED
GSE85977_hg18.HindIII.frag.bed.gz 7.4 Mb (ftp)(http) BED
GSE85977_readme.xlsx.gz 10.3 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data provided as supplementary file
Processed data are available on Series record
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