title: GSM8596716: 7dpf -28.5_Sox10:dsRed>GFP-2a-EWSFLI, GFP+, trunk, snATAC; Danio rerio; ATAC-seq
library_construction_protocol: Trunks from converted -28.5Sox10:Cre; actab2:loxP-BFP-STOP-loxP-DsRed (Sox10>DsRed) or -28.5Sox10:Cre;actab2:loxP-BFP-STOP-loxP-DsRed; Ubi:loxP-DsRed-STOP-loxP-GFP-2A-EF1 (Sox10>GFP-2A-EF1) fish at 7 dpf were cut posterior to ear and excluding swim bladder at all stages, cut into multiple pieces,  and placed in cold 1x PBS. Tumors from Sox10>GFP-2A-EF1 or normal tissue from control fish were dissected from young adult fish, cut into multiple pieces, and placed in cold 1x PBS. 1x PBS was then removed and replaced with pre-warmed Accumax. Samples were placed on a nutator at 30-32 °F, followed by mechanical dissociation by pipetting every 10 min (Innovative Cell Technologies Inc, AM105) for 1.5-2 hours. Cells were pelleted (200 × g, 10 min, 4 °C), supernatant was removed (leaving roughly 200 µL) and replaced with 1 mL of cold Hank's Buffer solution (0.25% BSA, 10mM HEPES, 1x HBBS). Cells were vortexed to resuspend and pelleted again (376 × g, 5 min, 4 °C), supernatant removed (leaving roughly 100 µL) and replaced with 100 µL of cold 1x PBS per 24 trunk reaction. Pellets were resuspended by vortexing and filtered through 40 µm strainers (Corning, 431750). Cells derived from fish at  7 dpf were resuspended, placed on ice and fluorescence-activated cell sorted (FACS) for DsRed (control) or GFP (EWSR1::FLI1+). All samples were subjected to nuclei isolation according to manufacturer's instructions (10x Genomics, protocol CG000169, “Low Cell Input Nuclei Isolation”). Multiome and snATACseq libraries were prepared using 10x Genomics Chromium Next GEM  Single Cell Multiome ATAC + Gene Expression or Chromium Next GEM Single Cell ATAC v2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq. Sequenced data was aligned using Cellranger-arc v2.0.2, Cellranger-atac v2.0.0, Cellranger v6.0.2  or Cellranger-arc v8.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.