scRNAseq of niPSC-OS1 cells in PDA83 for 24hrs
For 10x Genomics Chromium Single Cell sequencing, samples were multiplexed using 3' CellPlex Kit Set A. Single cell capture and library preparation was performed on a Chromium Controller using the Chromium GEM Single Cell 3 Kit version 3.1 as per the user guide, targeting a recovery of 3,000 cells per sample. We targeted a gene expression (GEX) coverage of 40,000-50,000 reads per cell, and 10,000-12,0000 reads per cell multiplex oligo. Sequencing was performed on a Novaseq 6000 instrument generating paired end reads (28x10x10x90 bases). Sample demultiplexing, alignment, and quantification of barcode counts was performed using CellRanger Multi.