In vitro growth signature identification from Chromium 10x sequencing of 5 human cancer cell lines and 1 mouse cancer cell line
The cell lines once in suspension were washed with PBS and pelleted by 5 minutes of centrifugation at 400g. The individual suspensions were filtered through a 35um mesh and their densities were adjusted to 106 cells/mL in PBS on ice. An equal volume of each suspension was pooled before being processed at the National Genomics Infrastructure (NGI, Scilifelab, Solna, Sweden). The cell processing consisted of proceeding with 10X Genomics V3.1 3' dual index protocol according to manufacturer instruction (10X Genomics) and the libraries produced were sequenced on a NovaSeq XPlus (Illumina). The Fastq files were analyzed using zUMIs using a combined mouse and human genome which was built with STAR and consisted of the genomes GRCh38 and GRCm38 (mm10), with additional barcode capture (see yaml files in Code repository).  The hashing barcodes were extracted using the tool UMIcountR29 and assigned to each cell. Based on the hashing barcodes and human and mouse gene usage per cell, cells were classified into the six conditions sequenced.