The raw fastq files of single-cell gene expression, feature barcode, and VDJ sequencing were processed using the multi pipeline of 10X Genomics’ Cell Ranger (5.0.0) software with GRCh38 reference genome (Cell Ranger GRCh38 Reference — 5.0.0). The output filtered feature-barcode matrices were input to R software (v3.6.2) with Seurat package (v3.2.0) for downstream analysis.37 Cells with < 300 or > 9000 genes, < 500 or > 50,000 UMIs, or > 10% mitochondrial UMIs were filtered out. Cell types were identified using SingleR package with “MonacoImmuneData” as reference.38,39
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