scATAC library of Donor PTID2 at week 3 Lane L002
To remove dead cells, debris, and neutrophils prior to scATAC-seq as described previously (Swanson et al. 2021),scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC v1.1 Reagent Kits User Guide (CG000209 Rev B) with several modifications. 15,000 cells were loaded into each tagmentation reaction. GEMs were separated into a biphasic mixture through addition of Recovery Agent (10x Genomics, 220016), the aqueous phase was retained and removed of barcoding reagents using Dynabead MyOne SILANE (10x Genomics, 2000048) and SPRIselect reagent (Beckman Coulter, B23318) bead clean-ups. Sequencing libraries were constructed by amplifying the barcoded ATAC fragments in a sample indexing PCR consisting of SI-PCR Primer B (10x Genomics, 2000128), Amp Mix (10x Genomics, 2000047) and Chromium i7 Sample Index Plate N, Set A (10x Genomics, 3000262) as described in the 10x scATAC User Guide.