Chromium next gem single cell 3 gem kit v3

10,000 nuclei were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM chip G Single Cell Kit (10X Genomics, PN-1000120) to generate single-cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, PN-1000121). The cDNA and library were made using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and Single Index Kit T Set A (10X Genomics, PN-120262) according to the manufacturer’s protocol. Quality control for the libraries was performed using Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) for qualitative analysis. Libraries were sequenced on an Illumina Novaseq 6000 system with 2 × 150 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, 8 bp I7 index for sample index and 91 bp Read2 for transcript.

Following manufacturer’s protocol the Chromium Controller (10X Genomics, PN-120223) was used to load 30,000 cells into a Chromium Next GEM chip G Single Cell Kit (10X Genomics, PN-1000120) to generate single cell gel beads in the emulsion (10X Genomics, PN-1000121). The cDNA and library were created using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) and Single Index Kit T Set A (10X Genomics, PN-120262), respectively⁵⁰ .