title: GSM1265805: WCE_9_4_12; Homo sapiens; ChIP-Seq
library_construction_protocol: 20-100 million target cells were cross-linked at room temperature for 10 min with fresh 11% formaldehyde, quenched with 2.5M glycine, and processed through the DNA elution steps following the Agilent Technologies Mammalian ChIP-on-chip protocol (version 10.2, March 2011, http://www.chem.agilent.com/Library/usermanuals/Public/G4481-90010_MammalianProtocol_10.2.pdf), with the following modifications: sonication buffer composition 20 mM Tris-HCl , 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100; sonication in 3 mL was performed on a Bioruptor Standard (Diagenode, Denville, NJ)  high setting at 4°C for 30 min total (cycles: 30 seconds on/30 seconds off); after sonication and centrifugation at 1400g, supernatant underwent immunoprecipitation with 10 ug antibody [anti-ZFXH4 (Abnova, H00079776-M11), mouse IgG2A (R&D Systems, AB003), anti-CHD4 (Abcam, ab72418), or rabbit polyclonal (Abcam, ab27478) antibodies] for four days for ZFHX4/mouse isotype control IP or overnight for CHD4/rabbit polyclonal control IP; protein G Dynabeads (Life Technologies, 1007D) were incubated with the IP lysates for 45 min and washed with sonication buffer x 2, buffer 1 (20 mM Tris HCl, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) x 2, buffer 2 (10 mM Tris HCl, 250 mM LiCl, 2 mM EDTA, 1% Igepal) x 2, and buffer 3 (10 mM Tris HCl, 1 mM EDTA, 50 mM NaCl) x 2. Immunoprecipitated DNA was quantified by picogreen and size was evaluated on a HighSense BioAnalyzer chip. Fragments between 100 and 600 bp were collected using an automated system (Pippin Prep, Sage Science) then end repaired, ligated and amplified for 15 cycles using reagents included in the Truseq DNA Sample Preparation kit from Illumina. Experimental conditions followed strictly the instructions of the manufacturer, with the exception of the adaptors being diluted 1/10 for the input DNA and 1/50 for all other samples. 7 barcoded libraries were run on 2 lanes of a Hiseq 2000 in a 50bp/50bp paired end run, using the TruSeq SBS Kit v3 (Illumina). The average number of read pairs per sample was 48 million
attributes.tag: GEO Accession
attributes.value: GSM1265805