GSM1944734: Runx1 ChIP-seq Replicate 2; Mus musculus; ChIP-Seq
H3K27Me3 ChIP samples were fixed using a 1% formaldehyde (FA) fixation protocol for 10 min, while a 60 min, 2 mM DSG and a 60 min 1% FA double fixation protocol was used for Ezh2 and Runx1 antibodies. Fixed chromatin samples were fragmented using a S220 Focused-ultrasonicators (Covaris) for 10 min with 10% duty cycle, 5 intensity, 200 cycle per burst with frequent sweeping mode and constant degassing at 4°C to an average size of 200-500bps. Antibody:chromatin complexes were collected with a mixture of protein A and Protein G Dynabeads (Life Technologies) collected with a magnet, and washed 3X with a solution of 50 mM HEPES-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate. After a TE wash, samples were eluted, de-crosslinked, RNase and Proteinase K treated, and purified using a QIAGEN PCR purification kit. ChIP samples were quantified relative to inputs. A 50 μl aliquot taken from each of 1 ml of sonicated, diluted chromatin before antibody incubation serves as the input, thus the signal from the input samples represents 5% of the total chromatin used in each ChIP. The library prep was performed on the Apollo system (Wafergen) with the kit PrepX Complete ILMN 32i DNA Library Kit (cat # 400076) and custom adapters.
GEO Accession
GSM1944734