GSM7104982: 1398P2, RPR2;Nfibf/f, lung tumor, rep2; Mus musculus; ATAC-seq
To perform ATAC-seq with mouse SCLC cell lines, ~100,000 suspension cells/cell line were collected trypsinized and processed using the OMNI-ATAC-Seq protocol (Corces et al., 2017). Briefly, cells were washed with 1 ml of ice-cold ATAC-RSB buffer, centrifuged at 500rcf for 5 minutes at 4℃. Next, the pellets were resuspended in 100µl of chilled ATAC-RSB-LYSIS and incubated on ice for 3 minutes. Lysis was stopped by adding 1mL of ATAC-RSB-WASH to each sample which were again centrifuged for 5 minutes at 500rcf. The supernatant was removed, and the pellet was resuspended in 50µl of OMNI-ATAC Mix and incubated in a mixing (500rpm) thermoblock at 37℃ for one hour. Tagmented DNA was purified using a Qiagen MinElute Kit (#28204), with 21µl of elution buffer warmed to 55℃. Library amplification PCR was performed with the NEBNext Ultra II Q5 2X Master Mix (NEB #M0544S) using Nextera primers for 12 cycles. DNA concentration was measured using a Qubit DNA HS Assay (ThermoFisher #Q33230). Individual samples were pooled sequenced on an Illumina NextSeq500 using the 75bp kit in a paired end configuration.