Comment[ArrayExpressAccession]	E-GEOD-19708
MAGE-TAB Version	1.1			
Public Release Date	2010-01-01
Investigation Title	Jarid2 and PRC2, Partner in Regulating Gene Expression			
Comment[Submitted Name]	Jarid2 and PRC2, Partner in Regulating Gene Expression
Experiment Description	The Polycomb Group proteins foster gene repression profiles required for proper development and unimpaired adulthood, and comprise the components of the PRC2 complex including the histone H3 lysine 27 (H3K27) methyltransferase Ezh2. How mammalian PRC2 accesses chromatin is unclear. We find that Jarid2 associates with PRC2 and stimulates its enzymatic activity in vitro.  Jarid2 contains a Jumonji C domain, but is devoid of detectable histone demethylase activity. Instead, its artificial recruitment to a promoter in vivo resulted in co-recruitment of PRC2 with resultant increased levels of H3K27me2/3. Jarid2 co-localizes with Ezh2 and MTF2, a homologue of Drosophila Pcl, at endogenous genes in ES cells. Jarid2 can itself bind DNA and its recruitment in ES cells is interdependent with that of PRC2 as Jarid2 knockdown reduced PRC2 at its target promoters, and ES cells devoid of the PRC2 component EED are deficient in Jarid2 promoter access. In addition to the well-documented defects in embryonic viability upon down-regulation of Jarid2, ES cell differentiation is impaired, as is Oct4 silencing.  Examination of two factors  in ES cells			
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	Ku	Bernstein	Reinberg	Ku
Person First Name	Manching	Bradley	Danny	Manching
Person Email	MKU@mgh.harvard.edu			
Person Affiliation	MGH			
Person Address	MGH, 185 Cambridge St. CPZN-8400, boston, MA, USA			
Person Roles	submitter			
Protocol Name	P-GSE19708-2	P-GSE19708-1	P-GSE19708-3	
Protocol Description	Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired and 5' phosphorylated using END-It DNA End Repair Kit (Epicenter). Then, DNA was treated with Klenow fragment (3' to 5', exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp to 70bp (insert plus adaptor and PCR primer sequences) were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.	ES cell was cultured in 15% FCS/DMEM, supplemented with Pen/Strep, Glutamax, MEM non-essential amino acids, ESGRO and 2-mercaptoethanol. ES cells were passaged off feeder cells for ~2-3 passages before harvesting for ChIP experiments.	For BED files: reads (of 36bps) produced by the Illumina platform were aligned by MAQ. Sequences with more than a single best matche in the reference genome were discarded. We also created a map of ?unalignable? genomic positions to which no unique 36 base read could be uniquely aligned due inherent sequence redundancy for consideration in downstream processing. For WIG files: The short sequence reads correspond to the end of the DNA fragments in the library. Since the average size of the ChIP fragments is in the range of 200 bp, we extended the aligned reads in silico to a total length of 200 bases. The entire genome was divided to non-overlapping windows of 25bps. The signal in a given window was calculated as the number of extended reads that it fall within that window.	
Protocol Type	nucleic acid library construction protocol	grow	feature_extraction	
Experimental Factor Name	CHIP ANTIBODY			
Experimental Factor Type	chip antibody			
Publication Title	Jarid2 and PRC2, partners in regulating gene expression.			
Publication Author List	Li G, Margueron R, Ku M, Chambon P, Bernstein BE, Reinberg D			
PubMed ID	20123894			
Publication DOI	10.1101/gad.1886410			
Comment[SecondaryAccession]	GSE19708			
Comment[GEOReleaseDate]	2010-01-01			
Comment[ArrayExpressSubmissionDate]	2009-12-30			
Comment[GEOLastUpdateDate]	2013-02-26			
Comment[AEExperimentType]	ChIP-seq			
Comment[SecondaryAccession]	SRP001723			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR034100-SRR034101			
SDRF File	E-GEOD-19708.sdrf.txt