GSM7747461: ATAC_Th1_d3_WT_3; Mus musculus; ATAC-seq
Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers. FastATAC-Seq was performed according to a published protocol(Corces et al., 2016) 10,000 sorted cells were pelleted and washed with 50 μl 1x PBS. After pelleting the nuclei by centrifuging at 500 x g for 10 minutes at 4°C, the pellets were re-suspended in 50 μl transposase mixture (25 μl of 2x TD buffer, 2.5 μl of TDE1, 0.5 μl of 1% digitonin, 22 μl of nuclease-free water) (Illumina, #20034197 and Promega, #G9441) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37°C with shaking at 300 rpm for 30 minutes.  The fragmentalized DNAs were then purified using a QIAGEN MinElute kit (Qiagen, #28006) and amplified with appropriate cycles of PCR based on the amplification curve using NEBNext High-Fidelity 2x PCR Master Mix (NEB, #M0541) and SYBR Green I (Thermo Fisher Scientific, #S-7563). Once the libraries were purified using a QIAGEN PCR cleanup kit (Qiagen, #28106), they were further sequenced for 50bp paired-end reads on NovaSeq or NextSeq (Illumina).