title: GSM8801430: Multiplexed CD8ab+ IELs, Gene expression; Mus musculus; RNA-Seq
library_construction_protocol: CD8αβ+ IELs from three Ighasec+/‑ and Ighasec‑/‑ mice were isolated from the jejunal intraepithelial compartment. Isolated cells were stained with fluorochrome conjugated antibodies for fluorescence-activated cell sorting. For cell hash-tagging, TotalSeq-C hashtag antibodies were added to each sample individually during the cell surface staining. Cells were gated as follows: FSC, SSC, singlets, live, TCRβ+, CD4-, CD8α+, CD8β+. The samples were then sorted together directly into PBS supplemented with 2% FBS, spun down and reconstituted in 1X PBS (calcium- and magnesium-free) containing 0.04% BSA. Samples were loaded on 10x Chromium Controller (10x Genomics) immediately after sorting. Libraries were constructed for gene expression data and TCR repertoire using Chromium Next GEM Single Cell 5' Library kit (v1.1). Capture, library preparation and sequencing were performed at the University of Chicago Genomics Facility.