Comment[ArrayExpressAccession]	E-GEOD-47485
MAGE-TAB Version	1.1			
Public Release Date	2013-07-22
Investigation Title	H3K27me3 is maintained at a reduced level in Suz12(Bgal/Bgal) ESCs			
Comment[Submitted Name]	H3K27me3 is maintained at a reduced level in Suz12(Bgal/Bgal) ESCs
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series			
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	Boyer			
Person First Name	Laurie			
Person Mid Initials	A			
Person Email	lboyer@mit.edu			
Person Affiliation	Massachusetts Institute of Technology			
Person Phone	617 324-3335			
Person Fax	617 253-8699			
Person Address	Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA			
Person Roles	submitter			
Protocol Name	P-GSE47485-4	P-GSE47485-2	P-GSE47485-1	P-GSE47485-3
Protocol Description	RNA was prepared using Trizol, according to the manufacturer's instructions. The RNA was examined for quality by Bioanalyzer (Agilent). RNA-seq libraries were then prepared as described in Wamstad et al., 2012. Briefly, mRNA was purified and fragmented, first strand cDNA was synthesized, and the second strand was synthesized. The SPRI-TE Nucleic Acid Extractor by Beckman Coulter was then used to automate library preparation. Each sample was amplified for 18 cycles. The samples were then examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.	The ChIP protocol has been adapted from previous studies (Lee et al., 2006; Boyer et al., 2006, Creyghton et al., 2008) with the following modification: Diagenode Bioruptor was used to sonicate with 30 cycles of 30 sec on (high), 30 sec off. The samples were sonicated in 15ml polystyrene tubes at 4°C while samples were immersed in ice cold water. Millipore 07-449 antibody was used in the ChIP. The ChIP DNA was then used to prepare sequencing libraries as described in Schmidt et al., 2009. For this study, a 1:40 dilution of Single End read adapters (Illumina) was used in the ligation reaction. Each sample was amplified for 18 cycles. The samples were then examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.	ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates. Briefly, cells were grown in Knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). Cells were then preplated - plated on cell culture plates without gelatin for 20 minutes to allow the MEFs to attach and thus deplete the cell population of MEFs - before collection for ChIP.	ESCs were plated with irradiated murine embryonic fibroblasts (MEFs) and grown under typical ESC conditions on gelatinized tissue culture plates. Briefly, cells were grown in Knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibitory factor (LIF), non-essential amino acids, L-glutamine, and penicillin/streptomycin as previously described (Boyer et al., 2006). Cells were then preplated - plated on cell culture plates without gelatin for 20 minutes to allow the MEFs to attach and thus deplete the cell population of MEFs - before collection for RNA preparation.
Protocol Type	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol	growth protocol
Experimental Factor Name	STRAIN OR LINE	GENOTYPE		
Experimental Factor Type	strain or line	genotype		
Comment[SecondaryAccession]	GSE47485			
Comment[GEOReleaseDate]	2013-07-22			
Comment[ArrayExpressSubmissionDate]	2013-05-29			
Comment[GEOLastUpdateDate]	2013-07-22			
Comment[AEExperimentType]	ChIP-seq			
Comment[AEExperimentType]	RNA-seq of coding RNA			
SDRF File	E-GEOD-47485.sdrf.txt