title: GSM5026486: 20180911_17-ucar-001-run30_FASTQ_NZO-3mo-M-BM-253_GT18-10921_CGAGGCTG-CTCCTTAC_S6; Mus musculus; ATAC-seq
library_construction_protocol: Data is obtained from bone marrow of NZO/HILtJ mouse strain, hereafter NZO at ages 3 and 18 months.   Cells were stained with:   CD8 FITC, Clone 53-6.7 BD Bioscience Cat# 553031, used at 1:240 final concentration  CD3e PE, Clone 145-2C11 eBioscience (Now ThermoFisher) cat# 12-0031-85, used at 1:240 final concentration  CD62L PE-Cy7, Clone MEL-14 Tonbo Biosciences Cat# 60-0621-U100, used at 1:480 final concentration  CD44 APC-Cy7, Clone IM7 Tonbo Biosciences Cat# 25-0441-U100, used at 1:240 final concentration  and for 30 minutes at 4 degrees C. Propidium Iodide used for cell viability at 0.5ug/ml.   Then cells were sorted on a FACSAria II (BD Biosciences). Briefly, doublets were gated out, Viable PI- cells were gated, CD3e+, CD8+ cells were gated and subdivided into CD44 Low, CD62L High Naïve cells and CD44 High, CD62L+/- Memory cells. Up to 50,000 cells were sorted for ATAC-seq ATAC-seq libraries were prepared using 50,000 cells, as previously described (Buenrostro et al, 2015), with the following modifications: digitonin was added to the transposition reaction at a final concentration of 0.01%; the transposition reaction was purified using the Genomic DNA Clean & Concentrator-10 kit (Zymo Research Corporation); PCR amplification was carried out using the Nextera DNA Library Prep (Illumina) Index Adapters, Nextera PCR Master Mix, and PCR Primer Cocktail for 10 cycles of PCR; PCR reaction was purified using 1.7x SPRI beads (Agencourt AMPure XP, Beckman Coulter). Libraries were checked for quality and concentration using the DNA High-Sensitivity LabChip assay (Agilent Technologies) and quantitative  PCR (KAPA Biosystems), according to the manufacturer's instructions. Libraries were pooled and sequenced 75 bp paired-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2 reagents (Illumina).