GSM7978630: Mouse lungs, post-injury day 35, scATAC-seq; Mus musculus; ATAC-seq
Lung samples were minced, digested in 5 mg/mL each of collagenase II and IV (ThermoFisher Scientific, cat# 17101015 and 17104019) in serum-free Dulbecco's Modified Eagle Medium (DMEM) (ThermoFisher Scientific, cat# 11965092) at 37 oC for 30 min with gentle agitation, neutralized in DMEM with 10% v/v fetal bovine serum (FBS) (GeminiBio, cat# 100-106), and filtered at 100 μm. The resulting suspensions were centrifuged at 500g for 5 min to isolate cell pellets, incubated in RBC lysis buffer (Millipore Sigma, cat# 11814389001) for 5 min, neutralized in DMEM with 10% FBS, centrifuged, resuspended in PBS, and filtered at 40 μm to yield single-cell suspensions. Epigenomic samples were prepared from pooled single-nuclei suspensions using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, Chromium Next GEM Chip H Single Cell Kit, and Single Index Kit N, Set A (10X Genomics, cat# 1000175, 1000161, and 1000212) according to kit instructions. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.