GSM8868245: CD45neg TdT-positive cells; Mus musculus; RNA-Seq
Sorted breast tumor cells were resuspended in PBS with 0.04% BSA at a final concentration of approximately 1000 cells/μl. cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup.  Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads.  Samples cDNA concentration was determined using a Bioanalyzer. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell  Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.