alias: GSM1674824
title: GSM1674824: P19_H3K4me3_6h_ATRA; Mus musculus; ChIP-Seq
library_construction_protocol: F9 or P19 EC cells were fixed with 1% para-formaldehyde (Electron Microscopy Sciences) for 30 minutes at room temperature. ChIP assays were performed following previously described conditions: chromatin sonication and immunoprecipitation in lysis buffer (50mM Tris–Cl pH=8, 140mM NaCl, 1mM EDTA, 1% Triton, 0.1% Na-deoxycholate) complemented with protease inhibitor cocktail (Roche 11873580001); 2x washes with lysis buffer; 2x washes with lysis buffer containing 360mM NaCl; 2x washes with washing buffer (10mM Tris–Cl pH=8, 250mM LiCl, 0.5% NP-40, 1mM EDTA, 0.5% Na-deoxycholate); 2x washes with 1x TE; elution at 651C; 15 min in elution buffer (50mM Tris–Cl pH=8, 10mM EDTA, 1% SDS). RXRa has been immunoprecipitated with purified polyclonal antibodies generated by immunization of rabbits with the following peptide:mRXRa: PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC). RXRa ChIP assays were performed with 6x106 cells per time point; while histone modification marks were evaluated with 2x106 cells. FAIRE assays were performed as described previously (Giresi et al, 2007; Simon et al, 2012). qPCR-qualified ChIP assays were quantified (Qubit dsDNA HS assay kit; Invitrogen); then 10 ng of the ChIPed material was used for preparing Illumina sequencing libraries following a multiplexing approach (NEXTflexTM ChIP-seq Bioo Scientific;  ref: 514120). Prepared sequencing libraries were sequenced on the Illumina instrument HiSeq2000 (4 ChIP samples per lane). Regular Illumina pipelines were used for image processing and base calling. Sequence files were then aligned to the mouse genome assembly following by default parameters (mm9; Bowtie).
identifiers.namespace: GEO
identifiers.id: GSM1674824