GSM7680087: Spinal cord MNs, olig2dsRed, prdm16:gal4UASGFP -, prdm16-/- 5dpf, scRNAseq; Danio rerio; RNA-Seq
DsRed positive cells were isolated from 2 dpf or 5 dpf control, mecom mutant, or prdm16 mutant zebrafish embryos on an Tg(olig2:DsRed2) or Tg(prdm16::GFP);Tg(olig2:DsRed2) background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade, dissociated using papain, filtered, and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP-, DsRed2-, and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRanger(v5.0.1) pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome (build GRCz11). Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics).