Illumina short-read scRNA-seq of PC3E and GS689 cell mixture
Single-cell cDNA was generated using the Chromium Next GEM Single Cell 3 Kit v3.1 and Chip G Single Cell Kit (10x Genomics), following the first two steps (GEM generation, barcoding; post GEM-RT cleanup, cDNA amplification) of the Chromium Next GEM Single Cell 3 Reagent Kit v3.1 protocol (dual index, standard throughput). GEM-RT incubation was extended to 90 min, and the PCR elongation time was extended to 4 min. Initial PCR amplification included 12 cycles.  Approximately 25% (10 L) of the initial cDNA product was used to prepare the 3 gene expression library following the Chromium Next GEM Single Cell 3 Reagent Kit v3.1 protocol (dual index, standard throughput). Dual Index Kit TT Set A was used for sample index PCR. The library was sequenced on a NovaSeq 6000 (Illumina) using paired-end reads (28/10/10/91 cycles) per the manufacturers instructions.