title: GSM8217743: DN1_scATAC-seq_WT; Mus musculus; ATAC-seq
library_construction_protocol: Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on sort-purified Lin–TCRb–CD8–CD44hiCD25– DN1 cells from WT, Tcf1−/−, Tcf1−/−Lef1−/−, Runx1−/−Runx3+/–, Tle1+/–34–/– mice. The cells were 'stained' with DNA-barcoded, TotalSeq-C0301 anti-mouse hashtag antibodies against H-2 MHC-I (M1/42) and CD45 (30-F11) (BioLegend). Excess hashtag antibodies were removed through two rounds of washing with PBS. The 'hashtagged” cells of various genotypes were combined and loaded onto 10X Genomics Chromium Controller to generate single-cell Gel Beads in emulsion (GEM). Construction of gene expression libraries and cell surface protein libraries was performed using the 10X Genomics Chromium Next GEM Single Cell 5' library kit (PN-1000165), following the manufacturer's instructions. The resulting gene expression and cell surface protein libraries were combined at a molecular ratio of 9:1 and sequenced on Illumina's NovaSeq X plus platform in paired-end read mode, with a read length of 150 nucleotides at Admera Health. scATAC-seq libraries were constructed with 10X Genomics Chromium Next GEM Single Cell ATAC library kit (PN-1000175).  Libraries were quantified using a KAPA Library Quantification Kit (KK4835), assessed for quality using an Agilent Tapestation, and then sequenced on Illumina's NovaSeq X plus in paired-end read mode with the read length of 150 nucleotides at the Admera Health.