GSM4561822: DLD1 BRCA2-/- sgNeg_rep3; Homo sapiens; ATAC-seq
50K cells were pelleted at 800 x g and washed with 50mL of ice cold 1 x PBS followed by 2min treatment with 50 uL lysis buffer. After pelleting nuclei, nuclei were re-suspended in 50uL of transposition buffer (25uL of 2x TD buffer, 22.5ul of molecular biology grade water and 2.5uL Tn5 transposase (Illumina, cat# FC-121-1030) to tag the accessible chromatin for 45min at 37C. Tagmented DNA was purified with MinElute Reaction Cleanup kit and amplified with 5 cycles. Additional number of PCR cycles was determined from the side re-action and ranged from 10-12 total cycles of PCR. Two to three replicates were performed for each condition. Libraries were purified using QiaQuick PCR purification kit and eluted in 20uL EB buffer. Indexed libraries were assessed for nucleosome patterning on the Agilent TapeStation 2200 and paired-end sequenced (38bp+38bp) on Illumina NextSeq 550.
GEO Accession
GSM4561822