title: GSM8514622: OT-I_TbetKO_01; Mus musculus; ATAC-seq
library_construction_protocol: Frozen cells were thawed and washed once in cold PBS. 70,000-200,000 cells were lysed using the 10x single-cell ATAC lysis buffer and centrifuged for 10 min at 4ºC/500g. Transposition reaction was performed using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (FC-121-1030), using 12.5 µL 2x TD Buffer, 10.5 µL H2O, and 2 µL transposase per reaction, and incubated at 37ºC for 30min. TE Buffer was added to halt the transposition reaction, then the product was purified using Qiagen Minelute (28004). The elute underwent PCR using Phusion High-Fidelity PCR MasterMix (NEB, M0531S) as follows; 5 min of initial extension at 72ºC, followed by 16 cycles of PCR (98ºC/15s, 63ºC/30s, 72ºC/60s), followed by final extension (72ºC/3min). The resulting product was purified using AMPure XP Beads (A63881), eluted in 20 µL H2O, and quantified using a Quibit dsDNA HS Assay Kit (Invitrogen) and a High Sensitivity DNA chip run on a Bioanalyzer 2100 system. The final product was sequenced on a NovaSeq. For each bulk ATAC-seq library, adapters were trimmed, and fastq reads were aligned using Bowtie2 OMNI ATAC-seq (Corces et al. 2017)