Comment[ArrayExpressAccession]	E-GEOD-42560
MAGE-TAB Version	1.1											
Public Release Date	2013-07-13
Investigation Title	Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes											
Comment[Submitted Name]	Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes
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	Collas											
Person First Name	Philippe											
Person Email	geo@ncbi.nlm.nih.gov											
Person Affiliation	University of Oslo											
Person Address	Institute of Basic Medical Sciences, University of Oslo, PO Box 1112 Blindern, Oslo, Norway											
Person Roles	submitter											
Protocol Name	P-GSE42560-1	P-GSE42560-2	P-GSE42560-5	P-GSE42560-9	P-GSE42560-10	P-GSE42560-6	P-GSE42560-3	P-GSE42560-8	P-GSE42560-12	P-GSE42560-4	P-GSE42560-7	P-GSE42560-11
Protocol Description	log2 (ChIP/Input) with biweight mean of values subtracted ID_REF =  VALUE = log2(Cy5/Cy3) M-bM-^@M-^S biweight mean	The data were normalised using quantile normalisation with GenomeStudio ID_REF =  VALUE = quantile normalized Detection Pvalue = 	Labeling done by Nimblegen as per normal service protocol	Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays	Standard Illumina hybridization protocol	Hybridization done by Nimblegen as per normal service protocol	DMEM/F12, 10% FCS	RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.	ChIP of modified histones was done as described (SM-CM-8rensen et al 2010 Mol Biol Cell) using antibodies to H3K9me3 (Diagenode, pAb-056-050), H3K27me3 (Millipore, 07-449) and H3K4me3 (Abcam, Ab8580). In short, cells were cross-linked for 8 min with 1% formaldehyde and sonicated to ~400 bp fragments using a Bioruptor (Diagenode). Chromatin (100 M-5l at 0.5 A260 U/M-5l) was incubated with 2.4 M-NM-<g antibody coupled to Dynabeads Protein A (Invitrogen). ChIP material was washed, RNAse-treated, purified by phenol-chloroform isoamylalcohol extraction, amplified using the WGA4 kit (Sigma-Aldrich), cleaned up and eluted in MilliQ water. For ChIP of LMNA, cells were cross-linked as above and chromatin prepared by lysis (5 min on ice) and sonication (total of 45 min in a Bioruptor) in the following lysis buffer: 10 mM Tris-HCl, pH 7.5, 10 mM KCl, 2 mM EDTA, 1% Triton X-100, protease inhibitors. Chromatin (100 M-5l at 2 A260 U/M-5l) was incubated overnight at 4oC with 2.4 M-NM-<g anti-lamin A/C antibody (Santa Cruz, sc-7292) coupled to Dynabeads Protein A (Invitrogen). ChIP material was washed in lysis buffer and processed as for histone ChIPs. MeDIP was performed as described (SM-CM-8rensen and Collas, 2009. Meth Mol Biol 567, 249-262). In short, genomic DNA was purified and fragmented by probe sonication to 300-500 base pair fragments. Methylated fragments were immunoprecipitated using anti-5 mC antibodies (Diagenode). Immunoprecipitated (MeDIP) and input DNA was amplified by 14 PCR cycles using the WGA2 kit (Sigma-Aldrich) and cleaned up using the MinElute PCR purification kit (Qiagen). Input and MeDIP DNA were labeled with Cy3 and Cy5 respectively and hybridized on the same promoter arrays as those used for ChIP-chip.	histone ChIPs: ChIP of modified histones was done as described (SM-CM-8rensen et al 2010 Mol Biol Cell) using antibodies to H3K9me3 (Diagenode, pAb-056-050), H3K27me3 (Millipore, 07-449) and H3K4me3 (Abcam, Ab8580). In short, cells were cross-linked for 8 min with 1% formaldehyde and sonicated to ~400 bp fragments using a Bioruptor (Diagenode). Chromatin (100 M-5l at 0.5 A260 U/M-5l) was incubated with 2.4 M-NM-<g antibody coupled to Dynabeads Protein A (Invitrogen). ChIP material was washed, RNAse-treated, purified by phenol-chloroform isoamylalcohol extraction, amplified using the WGA4 kit (Sigma-Aldrich), cleaned up and eluted in MilliQ water. Lamin A/C ChIPs: For ChIP of LMNA, cells were cross-linked as above and chromatin prepared by lysis (5 min on ice) and sonication (total of 45 min in a Bioruptor) in the following lysis buffer: 10 mM Tris-HCl, pH 7.5, 10 mM KCl, 2 mM EDTA, 1% Triton X-100, protease inhibitors. Chromatin (100 M-5l at 2 A260 U/M-5l) was incubated overnight at 4oC with 2.4 M-NM-<g anti-lamin A/C antibody (Santa Cruz, sc-7292) coupled to Dynabeads Protein A (Invitrogen). ChIP material was washed in lysis buffer and processed as for histone ChIPs. MeDIP: MeDIP was performed as described (SM-CM-8rensen and Collas, 2009. Meth Mol Biol 567, 249-262). In short, genomic DNA was purified and fragmented by probe sonication to 300-500 base pair fragments. Methylated fragments were immunoprecipitated using anti-5 mC antibodies (Diagenode). Immunoprecipitated (MeDIP) and input DNA was amplified by 14 PCR cycles using the WGA2 kit (Sigma-Aldrich) and cleaned up using the MinElute PCR purification kit (Qiagen). Input and MeDIP DNA were labeled with Cy3 and Cy5 respectively and hybridized on the same promoter arrays as those used for ChIP-chip.	Scanning done by Nimblegen as per normal service protocol	Standard Illumina scanning protocol
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	labelling protocol	hybridization protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	array scanning protocol	array scanning protocol
Experimental Factor Name	CELL TREATMENT	CHIP ANTIBODY	CELL TYPE									
Experimental Factor Type	cell treatment	chip antibody	cell type									
Comment[SecondaryAccession]	GSE42560											
Comment[GEOReleaseDate]	2013-07-13											
Comment[ArrayExpressSubmissionDate]	2012-11-27											
Comment[GEOLastUpdateDate]	2013-07-16											
Comment[AEExperimentType]	transcription profiling by array											
Comment[AEExperimentType]	ChIP-chip by tiling array											
Comment[AEExperimentType]	methylation profiling by array											
SDRF File	E-GEOD-42560.sdrf.txt