Comment[ArrayExpressAccession]	E-GEOD-48122
MAGE-TAB Version	1.1									
Public Release Date	2013-06-20
Investigation Title	REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells									
Comment[Submitted Name]	REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells
Experiment Description	Genome-wide analysis of REST and Polycomb binding in Rest-/- and Eed-/- mouse embryonic stem (mES) cells showed that Rest was required for PRC1 recruitment to a subset of Polycomb regulated neuronal genes. Furthermore, we found that PRC1 can be recruited to Rest binding sites independently of CpG islands and the H3K27Me3 mark., and that PRC2 was frequently increased around Rest binding sites located in CpG-rich regions in the Rest2/2 mES cells. Published here: PLoS Genet 8(3): e1002494. doi:10.1371/journal.pgen.1002494 Examination of REST and Polycomb binding in Rest-/-, Eed-/-, and wt mES cells using ChIP-sequencing. Submitter cannot locate the raw data for GSM1169003, GSM1169004, GSM1169011, GSM1169012, GSM1169015, and GSM1169016.									
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	Lerdrup	Dietrich	Lerdrup	Landt	Agrawal-Singh	Bak	Tommerup	Rappsilber	Södersten	Hansen
Person First Name	Mads	Nikolaj	Mads	Eskild	Shuchi	Mads	Niels	Juri	Erik	Klaus
Person Email	mads.lerdrup@bric.ku.dk									
Person Affiliation	University of Copenhagen									
Person Phone	+45 35325747									
Person Address	Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloeesvej 5, Copenhagen N, Denmark									
Person Roles	submitter									
Protocol Name	P-GSE48122-3	P-GSE48122-2	P-GSE48122-1							
Protocol Description	High quality reads (Chastity score .= 0.6) were aligned to the mouse genome (mm9) using Eland (Illumina) allowing up to two mismatches within the first 32 bases. Reads not aligning uniquely to the mouse genome were removed. Aligned datasets were filtered for multiple reads at the same position occurring after PCR amplication. Where more than one read mapped to the same position and at the same strand duplicates were removed. The reads were extended to 200 bp length, and the number of reads at a given position was counted and saved as a fixedStep wig file with 100 bp resolution. Peak calling was done in CisGenome 1.2 using IgG samples as negative controls. Lists of peaks and further descriptions can be found here: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002494 Genome_build: mm9 Supplementary_files_format_and_content: aln: list of aligned reads. wig: fixedStep Wiggle file containing densities with 100 bp resolution of aligned and filtered reads.	Cells were fixed for 10 min in culture media containing 1% formaldehyde and were processed for ChIP as in Dietrich et al. (2007) EMBO J 26: 1637–1648. DNA from three parallel ChIPs were pooled and 10 ng was used for making ChIP-seq libraries. Libraries were generated according to Illumina recommendations and sequencing was done on a Genome Analyzer II (Illumina).	Mouse embryonic stem (mES) cells were cultured on 0.1% (w/v) gelatin-coated plates in Glasgow medium (Sigma) supplemented with glutamax-1 (Gibco), non-essential amino acids (Gibco), 50 mM 2-mercaptoethanol–PBS, 15% ES-cell-qualified FBS (Gibco) in the presence of 1,000 U/ml of LIF (Millipore), and 1% (v/v) pen/strep. In addition, the Rest2/2 and Wt control mES cells were cultured in the presence of feeder cells (Mitomycin C treated primary mouse embryonic fibroblasts). The mES Eed2/2 and Rnf22/2 mES cells were provided by Dr. Anton Wutz. The Rest2/2 and Wt control mES cells were provided by Dr. Zhou-Feng Chen and Dr. Helle Færk Jørgensen.							
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol							
Experimental Factor Name	CHIP ANTIBODY CATALOG #	CHIP ANTIBODY	CHIP ANTIBODY MANUFACTURER	GENOTYPE						
Experimental Factor Type	chip antibody catalog #	chip antibody	chip antibody manufacturer	genotype						
Publication Title	REST-mediated recruitment of polycomb repressor complexes in mammalian cells.									
Publication Author List	Dietrich N, Lerdrup M, Landt E, Agrawal-Singh S, Bak M, Tommerup N, Rappsilber J, S�dersten E, Hansen K									
PubMed ID	22396653									
Publication DOI	10.1371/journal.pgen.1002494									
Comment[SecondaryAccession]	GSE48122									
Comment[GEOReleaseDate]	2013-06-20									
Comment[ArrayExpressSubmissionDate]	2013-06-19									
Comment[GEOLastUpdateDate]	2013-06-21									
Comment[AEExperimentType]	ChIP-seq									
Comment[SecondaryAccession]	SRP026172									
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR908371-SRR908382									
SDRF File	E-GEOD-48122.sdrf.txt