The output Illumina base call files from both sequencing runs were merged and converted to FASTQ files using Cell Ranger software v2.0.1, which included Illumina’s bcl2fastq v2.19.1.403. FASTQ files of each mouse sample were converted to count matrices using Cell Ranger software, based on transcriptome reference of Mus musculus (mm10 1.2.0). Barcodes (25,707) were identified as cells, according to Cell Ranger’s algorithm of calling cell barcodes. This algorithm takes as input the expected number of recovered cells, which was set to 3000 cells in our study. It then orders all barcodes by their unique molecular identifier (UMI) content and computes the number of UMIs at the 99th percentile. All barcodes whose total UMI count was at most 1/10 of this number were referred to as low-quality cells and discarded.

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