title: GSM4138221: WT_diff T4_ATAC-seq; Homo sapiens; ATAC-seq
library_construction_protocol: Briefly, collected cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and the nuclei were pelleted and resuspended in Tn5 enzyme and transposase buffer (Illumina Nextera® DNA library preparation kit, cat# FC-121-1030). The Nextera libraries were amplified using the Nextera® PCR master mix and KAPA biosystems HiFi hotstart readymix (cat # NC0295239) successively. AMPure XP beads (Beckman Coulter cat# A63881) were used to purify the transposed DNA and the amplified PCR products. All libraries were sequenced on a 100 cycle paired-end run on an Illumina NOVAseq instrument. The resulting ATAC-seq libraries were sequenced on Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine and paired-end 50 bp reads were generated. Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim _galore/). The resulting high-quality reads were aligned to the human reference genome hg38 using bowtie2 (version 2.3.2) 63 with parameters “-X 2000 --no-mixed --no-discordant”.  Duplicate reads were discarded with Picard (https://broadinstitute.github.io/picard/). Reads mapped to mitochondrial DNA together with low mapping quality reads (MAPQ<10) were excluded from further analysis. All of ATAC-seq experiments were done in Department of Medical and Molecular Genetics at the Indiana University School of Medicine. And data analysis was finished in The Center for Medical Genomics at Indiana University School of Medicine.
attributes.tag: GEO Accession
attributes.value: GSM4138221