GSM5818614: AW20003_GT20-13864_SI; Homo sapiens; RNA-Seq
Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform (50) version 3.1 chemistry and according to the manufacturer's protocol (#CG00052) with modifications for generating the hashtag library(51). cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and pooled using a ratio of 95% gene expression library and 5% hashtag library before sequencing; each gene expression-hashtag library pair was sequenced at 50% of lan Illumina NovaSeq 6000 S2 flow cell lane, targeting 20,000 barcoded cells with an average sequencing depth of 50,000 reads per cell. Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina) and FASTQ files associated with the gene expression libraries were aligned to the GRCh38.93 reference genome (10x Genomics GRCh38 reference 3.0.0 [including all transcribed unitary pseudogenes]) using the version 3.1.0 Cell Ranger count pipeline (10x Genomics). FASTQ files representing the hashtag libraries were processed into hashtag-count matrices using CITE-Seq-Count (version 1.4.3) (https://zenodo.org/badge/latestdoi/99617772).