GSM5065087: OT-I; Mus musculus; RNA-Seq
F1(B6xBalb/c).OVA kidney allografts were harvested 1 or 5 weeks (n = 3 from each time point) after transplantation from B6 recipients that also received 1 x 10^6 effector DsRed+ OT-I cells on day 2. In vivo labelling was done using 3µg of anti-CD45 i.v. 2 min prior to sacrifice. Lin−(CD11c, CD11b, Ter119, CD16/32, B220, F4/80, DX5, NK1.1, Ly6g, CD19) and intravascular CD45+ cells were excluded from sorted cell population. Polyclonal CD45.1+dsRed−Thy1.2+CD5+ T cells and monoclonal CD45.1−dsRed+Thy1.2+CD5+ OT-I cells were sorted separately from each harvested graft. Each sorted polyclonal and OT-I T cell sample  was then labelled with cell hashing antibodies (Totalseq-A, Biolegend) (table S4) for later demultiplexing(64). Polyclonal and OT-I T cell samples were pooled separately and sequenced. scRNAseq was performed using 10X Genomics Single Cell 3′ solution, version 2, according to the manufacturer's instructions  with 7,000 sorted polyclonal or OT-I T cells loaded for each sample.  mRNA and hashtag oligos cDNA libraries from pooled samples were sequenced on the NextSeq500 Platform (Illumina). RNA libraries were prepared for sequencing using 10X Genomics Single Cell 3′ solution, version 2