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Series GSE80280 Query DataSets for GSE80280
Status Public on Mar 07, 2017
Title 3D structures of individual mammalian genomes reveal principles of nuclear organization
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary The folding of genomic DNA from the beads-on-a-string like structure of nucleosomes into higher order assemblies is thought to be critically linked to nuclear processes, but it is unclear to what degree it is a cause or consequence of function. We have calculated the first 3D structural models of entire mammalian genomes using data from a new chromosome conformation capture protocol that allows us to first image and then process single cells. This has allowed us to study the folding of chromosomes down to a sub-100 kb scale. We show that the structures of individual topological-associated domains, chromosomes, and the way they pack together, varies very substantially from cell-to-cell. However, in all cells we find a consistent large-scale organization of compartments, with active enhancers and promoters clustering near inter-chromosomal interfaces, suggesting that nuclear processes such as transcription may drive chromosome and genome folding.
 
Overall design ChIP-seq, RNA-seq and nuclear RNA-seq in haploid and diploid mouse embryonic stem cells
 
Contributor(s) Laue ED
Citation(s) 28289288
Submission date Apr 14, 2016
Last update date Mar 21, 2019
Contact name Andre J Faure
E-mail andre.faure@crg.eu
Organization name Centre for Genomic Regulation (CRG)
Department EMBL-CRG Systems Biology Unit
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (42)
GSM2123546 CTCF ChIP (haploid)
GSM2123547 SMC3 ChIP (haploid)
GSM2123548 H3K27me3 ChIP (haploid)
Relations
BioProject PRJNA318485
SRA SRP073306

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
GSE80280_Chd4_ESC_peaks.bed.gz 837.8 Kb (ftp)(http) BED
GSE80280_Mbd3_ESC_peaks.bed.gz 496.8 Kb (ftp)(http) BED
GSE80280_RAW.tar 19.7 Gb (http)(custom) TAR (of BED, HDF5, PDB, TSV, TXT, XYZ)
GSE80280_corr_Expression_Chd4.txt.gz 2.1 Mb (ftp)(http) TXT
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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