iPSC-CD4 generation and characterization

Raw fastq files from all samples were aligned and quantified using CellRanger (CellRanger 6.0.1) and aligned with the human genome reference hg38. Following the suggested pipeline for quality control in Scanpy (v 1.10.2), CITE-seq data were filtered for dead cells, doublets, and red blood cells by excluding cells with greater than 5% mitochondrial genes and less than 1000, but no more than 30000 genes. Genes found in less than 3 cells were removed. Samples underwent normalization, scaling, dimensional reduction, and further downstream analysis using the standard Scanpy workflow. Leiden clustering was performed using 50 principal components and a resolution of 0.5. Cells were clustered and identified based on known marker genes.