GSM3558603: TTC1240_ATAC_N106_SMARCB1_K364del_Rep2; Homo sapiens; ATAC-seq
ChIP-seq was performed using standard protocols (Millipore, Billerica, MA). Specifically, cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. All ChIP-seq was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. RNA was collected in biological duplicate using the RNeasy Mini Kit (QIAGEN). All RNA was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters. ATAC-seq libraries were prepared in biological replicates using standard protocol (Buenrostro et al., Current Protocols (2013)) with 12 cycles of amplification. ATAC-seq samples were sequenced on Nex-seq 500 using 37 bp, 37 bp pair-end sequencing parameters. ChIP-sequencing libraries were prepared with Illumina's NEBNext Ultra II DNA library Prep Kit using standard protocols. RNA-seq libraries were prepared with Illumina's TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).
GEO Accession
GSM3558603