GSM9168539: Pt 'AML15', unenriched BMA, HLA transcripts captured from cell-barcoded whole RNA; Homo sapiens; OTHER
scrHLA-typing's starting material is unfragmented cell-barcoded (CB) whole transcriptome cDNA from single-cell RNA-seq libraries (e.g., those generated by 10x Genomics). Briefly, cDNA is incubated with custom-designed 5-prime biotinylated DNA oligonucleotides HLA-specific (HLA hybridization probes) and blocking oligos to prevent PCR artifacts. After incubation, the biotinylated probes are bound to streptavidin magnetic beads, allowing for the enrichment of HLA target sequences. These molecules are then PCR-amplified and long-read sequenced. Long-read sequencing involves constructing PacBio SMRTbells using PacBio SMRTbell Prep kit 3.0 (PacBio #102-141-700), as per manufacturer's protocol (PacBio Procedure & Checklist #102-359-000 REV03 DEC2023). Libraries are sequenced on a PacBio Sequel IIe with 2 hours pre-extension time and 30 hours movie time. scrHLA-typing