Comment[ArrayExpressAccession]	E-GEOD-43922
MAGE-TAB Version	1.1								
Public Release Date	2013-01-31
Investigation Title	H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence								
Comment[Submitted Name]	H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence
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	Chicas								
Person First Name	Agustin								
Person Email	agustin_chicas@H3biomedicine.com								
Person Affiliation	Memorial Sloan Kettering								
Person Address	Memorial Sloan Kettering, One Bungtown Road, Cold Spring Harbor, NY, USA								
Person Roles	submitter								
Protocol Name	P-GSE43922-1	P-GSE43922-5	P-GSE43922-6	P-GSE43922-2	P-GSE43922-8	P-GSE43922-9	P-GSE43922-4	P-GSE43922-3	P-GSE43922-7
Protocol Description	The data were analyzed with the GC-RMA (Robust Multi-Array Averaging with GC content correction) method of the Bioconductor R package to subtract background, normalize intensities and summarize gene expression levels. ID_REF =  VALUE = Bioconductor GC-RMA signal intensity	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Hybridization to Human Gene ST 1.0 GeneChips (Affymetrix) was as described in Expression Analysis Technical Manual Affymetrix P/N 702232 Rev 2 (16 hours, 45 degress at 60 rpm). The Wash and Stain Protocol was as described in FS450_0004 using GeneChip Hybridization, Wash and Stain Kit.	Human fibroblast (IMR90) cells were infected with retroviral vectors expresssing shRNA targeting Jarid1, Jarid1b or both, and triggered to undergo quiescence by removal of serum or senescence by over-expression of activated ras (Hrasv12).	IMR90 cells were infected with Ras vector and the indicated hairpins. The cells were collected 7 days after puromycin selection.	The ChIP experiments were done as previously described (Chicas et al. 2010 (PMID 20385362)) using anti-H3K4me3 antibody (Millipore #05–745; 1:500). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.	Total RNA was extracted with the RNeasy Mini Kit (QIAGEN) and utilized for cRNA expression with Message Amp II (Ambion).	Human IMR90 cells with different conditions were grown at 37C at 5% CO2. Total RNA was extracted seven (7) days after the end of puromycin selection.	Scanning was performed using the Affymetrix GeneChip Scanner 3000.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	sample treatment protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol	array scanning protocol
Experimental Factor Name	GROWTH STATE	SHRNA							
Experimental Factor Type	growth state	shRNA							
Publication Title	H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence.								
Publication Author List	Chicas A, Kapoor A, Wang X, Aksoy O, Evertts AG, Zhang MQ, Garcia BA, Bernstein E, Lowe SW								
PubMed ID	22615382								
Publication DOI	10.1073/pnas.1119836109								
Comment[SecondaryAccession]	GSE43922								
Comment[GEOReleaseDate]	2013-01-31								
Comment[ArrayExpressSubmissionDate]	2013-01-30								
Comment[GEOLastUpdateDate]	2014-03-13								
Comment[AEExperimentType]	transcription profiling by array								
Comment[AEExperimentType]	ChIP-seq								
SDRF File	E-GEOD-43922.hyb.sdrf.txt	E-GEOD-43922.seq.sdrf.txt