GSM7663333: Kabuki syndrome type 2 replicate 2 [102T-KDM6a]; Mus musculus; ATAC-seq
T cells were isolated at the same time as B cells (Luperchio, Boukas et al. 2021). Specifically, flow through from binding and washing of CD19+ cells on Miltenyi separation columns was collected on ice. These CD19+ depleted samples were then spun and the supernatant was aspirated, resuspended and incubated with 2x (20uL) CD90.2+ microbeads (Miltenyi Biotec 130-121-278). CD90.2+ T cells were bound, washed and eluted per manufacturer protocol, then counted and aliquoted on ice for subsequent processing. Further processing of the T cell samples and ATAC sequencing was done in parallel with B cells. Samples were resuspended in tagmentation reaction mix for 30 min (2.5uL TD1, 1X TD Buffer, Illumina Nextera DNA, FC-121-1030; .25uL 1% digitonin, Promega G9441; 1xPBS) gently shaking (300rpm on Eppendorf thermomixer) at 37'. We purified reactions using Zymo DNA Clean and Concentrator-5 kit (Zymo D4013) following manufacturer protocols and eluted with 10.5uL water to recover 10uL. Each reaction was then amplified and indexed per standard ATAC-seq protocol. After indexing and amplification, we purified samples using Select-A-Size purification columns (Zymo D4080) with a cutoff of 150bp to remove adapter dimers to allow for efficient sequencing on patterned flow cells, checked library size on BioAnalyzer using DNA High Sensitivity reagents (Agilent 5067-4626) and determined concentration using Qubit dsDNA HS Assay Kit (ThermoFisher Q32851).