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Series GSE35156 Query DataSets for GSE35156
Status Public on Apr 10, 2012
Title Conserved Topological Domains in Mammalian Genomes Identified by High-resolution Analysis of Chromatin Interactions
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is limited. Here we present high-resolution analyses of chromosomal organization in pluripotent and differentiated human and murine cell types determined using the Hi-C technique. We find that the mammalian genome is composed of over 1000 topological domains, which are stable among different cell types and highly conserved across species. These megabase-long genomic structures, defined by prominent local chromatin interactions and separated by narrow boundary regions, likely function to restrict regulatory interactions between cis-acting elements and limit the spreading of heterochromatin during cellular differentiation. Interestingly, the boundaries are enriched not only for binding sites of the insulator protein CTCF, but also for promoters of house keeping genes, supporting a role for both CTCF and housekeeping genes in the establishment or maintenance of the topological domains.
 
Overall design Hi-C experiment were conducted in mESC, hESC and IMR90 cells
 
Contributor(s) Dixon J, Ren B
Citation(s) 22495300
Submission date Jan 17, 2012
Last update date May 15, 2019
Contact name Feng Yue
E-mail(s) fyue@ucsd.edu
Organization name Ludwig Institue for Cancer Research
Street address 9500 Gilman Dr.
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (9)
GSM862720 RenLab-HiC-mESC-HindIII, replicate one
GSM862721 RenLab-HiC-mESC-HindIII, replicate two
GSM862722 RenLab-HiC-mESC-NCoI
Relations
SRA SRP010370
BioProject PRJNA150781

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
GSE35156_GSM862720_J1_mESC_HindIII_ori_HiC.nodup.hic.summary.txt.gz 8.5 Gb (ftp)(http) TXT
GSE35156_GSM862721_J1_mESC_HindIII_rep_HiC.nodup.summary.txt.gz 5.7 Gb (ftp)(http) TXT
GSE35156_GSM862722_J1_mESC_NcoI_HiC.nodup.hic.summary.txt.gz 7.0 Gb (ftp)(http) TXT
GSE35156_GSM862723_hESC_HindIII_HiC.nodup.summary.txt.gz 1.6 Gb (ftp)(http) TXT
GSE35156_GSM862724_IMR90_HindIII_HiC.nodup.summary.txt.gz 6.0 Gb (ftp)(http) TXT
GSE35156_GSM892304_cortex_HindIII_ori_HiC.nodup.hic.summary.txt.gz 6.4 Gb (ftp)(http) TXT
GSE35156_GSM892305_cortex_HindIII_replicate_Hic.nodup.hic.summary.txt.gz 5.1 Gb (ftp)(http) TXT
GSE35156_GSM892306_hESC_HindIII_HiC_replicate.nodup.hic.summary.txt.gz 7.7 Gb (ftp)(http) TXT
GSE35156_GSM892307_IMR90_HindIII_HiC_replicate.nodup.hic.summary.txt.gz 4.9 Gb (ftp)(http) TXT
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