Comment[ArrayExpressAccession]	E-GEOD-48965
MAGE-TAB Version	1.1									
Public Release Date	2013-12-11
Investigation Title	Cohesin is a key determinant of interphase chromosome domain architecture (RNA-seq)									
Comment[Submitted Name]	Cohesin is a key determinant of interphase chromosome domain architecture (RNA-seq)
Experiment Description	To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. These loops demarcate topological domains and form intricate internal structures within them. Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains. Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes. Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programs within them. Hi-C, ChIP-Seq and RNA-Seq experiments were conducted in mouse neural stem cells and mouse astrocytes									
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl								
Person Last Name	Hadjur	Sofueva	Yaffe	Chan	Georgopoulou	Vietri-Rudan	Pollard	Schroth	Tanay	Hadjur
Person First Name	Suzana	Sevil	Eitan	Wen-Ching	Dimitra	Matteo	Steven	Gary	Amos	Suzana
Person Mid Initials							M	P		
Person Email	s.hadjur@ucl.ac.uk									
Person Affiliation	Ucl									
Person Phone	+44 7798957199									
Person Address	Cancer biology, Ucl, 72 Huntley street, London, United Kingdom									
Person Roles	submitter									
Protocol Name	P-GSE48965-1	P-GSE48965-3	P-GSE48965-2							
Protocol Description	To delete Rad21, cells were treated with AdCre for 72 or 96hr	RNA was extracted using qiagen RNAeasy columns. Cells were treated with accutase, washed and immediately flash frozen. RNA was prepared using standard protocols and only high quality RNA (RIN>8) was used downstream. RNA was fragmented, PE adapters were ligated and libraries amplified according to the Illumina TruSeq protocol	Cells were grown in serum-free media containing BMP+FGF and Laminin							
Protocol Type	sample treatment protocol	nucleic acid library construction protocol	growth protocol							
Experimental Factor Name	TIME	GENOTYPE								
Experimental Factor Type	time	genotype								
Publication Title	Cohesin-mediated interactions organize chromosomal domain architecture.									
Publication Author List	Sofueva S, Yaffe E, Chan WC, Georgopoulou D, Vietri Rudan M, Mira-Bontenbal H, Pollard SM, Schroth GP, Tanay A, Hadjur S									
PubMed ID	24185899									
Publication DOI	10.1038/emboj.2013.237									
Comment[SecondaryAccession]	GSE48965									
Comment[GEOReleaseDate]	2013-12-11									
Comment[ArrayExpressSubmissionDate]	2013-07-17									
Comment[GEOLastUpdateDate]	2013-12-11									
Comment[AEExperimentType]	RNA-seq of coding RNA									
Comment[AdditionalFile:Data1]	GSE48965_RNA_mAST.genes.fpkm_tracking									
Comment[SecondaryAccession]	SRP027571									
SDRF File	E-GEOD-48965.sdrf.txt