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Series GSE48262 Query DataSets for GSE48262
Status Public on Sep 26, 2013
Title Single cell Hi-C reveals cell-to-cell variability in chromosome structure
Organism Mus musculus
Experiment type Other
Summary Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation, affecting most domains in most nuclei. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns.
Overall design Mouse Th1 single-cell Hi-C maps were produced and paired-end sequenced. 10 single-cell samples and a multi-sample pool together with a population Hi-C sample are included.
Contributor(s) Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P
Citation(s) 24067610
Submission date Jun 25, 2013
Last update date May 15, 2019
Contact name Yaniv Lubling
Organization name Weizmann Institute of Science
Street address POB 26
City Rehovot
ZIP/Postal code 76100
Country Israel
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL15103 Illumina HiSeq 1000 (Mus musculus)
Samples (11)
GSM1173492 Th1 ensemble Hi-C
GSM1173493 cell-1
GSM1173494 cell-2
BioProject PRJNA209421
SRA SRP026294

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE48262_RAW.tar 304.1 Mb (http)(custom) TAR (of TXT)
GSE48262_Th1_bgl_pool.txt.gz 19.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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