scRNA-Seq of Homo sapiens: T-ALL cells
Whole transcriptome analyses at single cell level and profiling of 42 oligoconjugated antibodies were performed on FACS-sorted primary T-ALL cells using the BD Rhapsody Single-Cell Analysis System (BD, Biosciences). Isolated cells from each sample were labeled with the BD Single-Cell Multiplexing Kit (cat. 633781, BD Biosciences) and the BD AbSeq Ab-Oligos for 1 hour following the manufacturers protocol. Afterward leukemia cells for each sample at the diagnosis (d0) (BD sample Tag.1) and after treatment (d30) (BD sample Tag.2) were pooled equally in 650ml cold BD Sample Buffer and three BD Rhapsody cartridges were loaded with 10,000 pooled cells for single cell separation. Single cells were isolated using Single-Cell Capture and cDNA Synthesis with the BD Rhapsody Express Single-Cell Analysis System according to the manufacturers recommendations (BD Biosciences). Sequencing was performed in paired-end mode (2*75 cycles) on NextSeq 500 System (Illumina) with the NextSeq 500/550 High Output Kit v2.5 (150 Cycles) chemistry to reach a depth of 75,000 reads for WTA, 21,500 reads for AbSeq and 500 reads for SMK per cell for a total of 97,000 reads per cell on average.