GSM5518395: hichip-P-D2; Homo sapiens; OTHER
The HiChIP protocol was performed for Astrocytes, ESC cells, N-D2, N-D4, N-D10, and N-D28 as previously described (Mumbach 2016) using antibody H3K27ac (Abcam, ab4729) with the following modifications. Samples were sheared using a Covaris E220 using the following parameters: Fill Level = 10, Duty Cycle = 5, PIP = 140, Cycles/Burst = 200, Time = 4 minutes and then clarified by centrifugation for 15 minutes at 16100 rcf at 4° C.  We used 4 ug of antibody to H3K27ac and captured the chromatin-antibody complex with 34 uL Protein A beads (Thermo Fisher). Qubit quantification following ChIP ranged from 125-150 ng. The amount of Tn5 used and number of PCR cycles performed were based on the post-ChIP Qubit amounts. HiChIP samples were size selected by PAGE purification (300-700 bp) for effective paired-end tag mapping and where therefore removed of all primer contamination. All libraries were sequenced on the Illumina NovaSeq 6000 instrument to an average read depth of 300 million total reads. H3K27ac HiChIP