title: GSM1399261: Total input of ChIP: LV sh-TRIM28 transduced ES cells; Homo sapiens; ChIP-Seq
library_construction_protocol: ES cell samples were washed 2x (in KO medium), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde at RT), quenched with glycine at 125mM, incubated 5' on ice, washed 3x (cold PBS) and pelleted at 10e7 cells per ependorf. Pellets were lysed according to Covaris protocol: pellets were resuspended in ice cold buffer 1 (50mM HEPES-KOH pH7.4, 140mM NaCl, 1mM EDTA, o.5mM EGTA, 10% glycerol, 0.5% NP40, 0.25% TX100, antiproteases), then in ice cold buffer 2 (10mM Tris pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, antiproteases) then washed 3 times and resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to TC12 glass tubes (Covaris: 520056) and sonicated (Covaris settings: 20% duty cycle, intensity 5, 200cyles/ burst, 40 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification and quality control on a Bioanalyzer (Agilent 2100). Samples were also checked for the absence of single-stranded DNA by Exonuclease I treatment and the sonicated samples were used for further chromatin immunoprecipitation Libraries were prepared according to Illumina's instructions. 10ng ChIPed DNA was used
identifiers.namespace: GEO
identifiers.id: GSM1399261