alias: GSM1563246
title: GSM1563246: RAD23B_Xpc-/-_ChIP3; Mus musculus; ChIP-Seq
library_construction_protocol: Crosslinked cells were resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40) and incubated for 10' on ice.  Lysates were dounced 10 times using a homogenizer andnuclear pellets were resuspended in sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 1% SDS), incubated on ice for 10', and sonicated to obtain DNA fragments averaging 100 to 300 bp in length (Covaris S-system). ChIP-seq: Libraries were prepared with the Illumina ChIP-seq DNA sample preparation kit according to manufacturer instructions with few modifications.  The material equivalent to 4 normal ChIPs was pooled to a final volume of 50 μl, 30 μl of which were further processed.  Fragments ranging from 150 to 350 bp in size were selected from gel prior to PCR amplification instead of the suggested 200 ±25 bp range.  Size, purity, and concentration of the sample were checked by Agilent Technologies 2100 Bioanalyzer and submitted for sequencing RNA-seq: 6 μg of total RNA were used to prepare poly-A libraries following the TruSeq™ RNA Sample Preparation Guide (Illumina). Libraries were indexed with the following TruSeq adapters: WT JM8.N4 mESCs: AR005-ACAGTG(A); Rad23b-/- JM8.N4 mESCs: AR006-GCCAAT(A); SCC KD1 JM8.N4 mESCs: AR012-CTTGTA(A); SCC KD2 JM8.N4 mESCs: AR019-GTGAAA(C)  Libraries were checked for quality and concentration by Bioanalyzer (2100 DNA, Agilent Technologies), Qubit (Life Technologies) and qPCR and sequenced in one lane of the HiSeq2000 platform (single-end reads, 50 bp; Illumina).
identifiers.namespace: GEO
identifiers.id: GSM1563246
attributes.tag: GEO Accession
attributes.value: GSM1563246