GSM7085290: 10X_22_016, 5 days post double ablation; Danio rerio; RNA-Seq
Droplet-based scRNA-seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10× Genomics) and Chromium Single Cell 3′ Chip G (10× Genomics). Approximately 8,000-10,000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA-Seq libraries were PCR amplified (13 cycles), pooled, denatured, and diluted in prior to paired-end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome (GRCz11) with addition of the mCherry sequence using Cell Ranger v5.0.1 (10× Genomics) to generate a gene-by-cell count matrix with default parameters.