GSM6285671: ARID1a KNOCKDOWN +DEX 2 [ATAC-seq]; Homo sapiens; ATAC-seq
HeLa cells were detached from flasks using Accutase, then resuspended in PBS at 6 million cells/ml. Nuclei were isolated and ATAC was performed following methods previously described. Transposition was achieved using Nextera Tn5 Transposase (Nextera kit). ATAC-Seq samples were pooled and sequenced on NextSeq using TruSeq Chip Samples Prep Kit (IP-202-1012) and paired-end sequencing.  All the samples have percent of Q30 bases above 87%. All the samples have yields between 89 and 135 million pass filter reads. Samples were trimmed for adapters using trimmomatic software before the alignment. The trimmed reads were aligned with Human - hg19 reference using Bowtie2 alignment. Overall alignment percentage for the samples is 98%. Unique alignment is above 53%. There are 1.79 to 2.17% unmapped reads. Library complexity is measured by uniquely aligned reads using picard's markduplicate utility. All the samples have library complexity with percent non-duplicated reads ranging from 47 to 61%.