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Series GSE77553 Query DataSets for GSE77553
Status Public on Feb 04, 2016
Title Capturing pairwise and multi-way chromosomal conformations using C-walks
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs), are highly conserved between cell types and species. Whether pairwise loops synergize to form higher order structures is still unclear. Here we develop a conformation capture approach to study higher order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains. The data captured a hierarchical chromosomal structure at varying scales. Inter-chromosomal contacts constitute only 7-10% of the pairs and are restricted by the TAD structure of the interfacing chromosomes. About half of the C-walks stay within one chromosome, and almost half of these are restricted to intra-TAD spaces. Analysis of nested topological motifs suggests hierarchical chromosomal structure is present also within TADs. Targeted analysis of thousands of 3-walks anchored at strongly expressed genes support nested, rather than hub-like, chromosomal topology at active loci. Polycomb-repressed HOX domains are shown by the same approach to form synergistic hubs. Together, the data suggest that chromosomal territories, TADs, and intra-TAD loops are primarily driven by nested, possibly dynamic, pairwise contacts.
 
Overall design Unbiased shotgun sequencing of 1pg samples of chromosome conformation campture (3C) template for the assembly of chromosome walks (c-walks) on K562 and mES in addition to 3-way 4C for the assesment of active chromatin hubs (human;K562) and polycomb domains on HOX gene clusters (mouseES).
Hi-C (mouseES) : in-nucleus ligation 3C; biotin fill-in was omitted. Digested with 15 ┬Ál HC DpnII (NEB 50,000 U/ml).
 
Contributor(s) Olivares-Chauvet P, Tanay A
Citation(s) 27919068
Submission date Feb 03, 2016
Last update date May 15, 2019
Contact name Pedro Olivares-Chauvet
E-mail(s) pedro@weizmann.ac.il
Organization name Weizmann Institute of Science
Department Department of Computer Science and Applied Mathematics/Department of Biological Regulation
Street address 234 Hertzl Street
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platforms (8)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (20)
GSM2054402 Cwalk library from 1pg of 3C template amplified with Phi29 (ms_k562_I)
GSM2054403 Cwalk library from 1pg of 3C template amplified with Phi29 (hs_k562_I)
GSM2054404 Cwalk library from 1pg of 3C template amplified with Phi29 (hs_k562_II)
Relations
BioProject PRJNA310778
SRA SRP069257

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
GSE77553_RAW.tar 3.6 Mb (http)(custom) TAR (of TXT)
GSE77553_k562.cadj.annot.txt.gz 193.2 Mb (ftp)(http) TXT
GSE77553_k562.tadj.txt.gz 3.2 Mb (ftp)(http) TXT
GSE77553_mesc.cadj.annot.txt.gz 248.9 Mb (ftp)(http) TXT
GSE77553_mesc.tadj.txt.gz 1.6 Mb (ftp)(http) TXT
GSE77553_mesc_hic.adj.txt.gz 2.7 Gb (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

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