GSM5651459: 36 hpf Zebrafish VDA scATAC_seq; Danio rerio; ATAC-seq
For 10x Genomics-based scRNA-seq and scATAC-seq in zebrafish, 40,000 mCherry+ GFP- cells, 40,000 mCherry+ GFP+ cells and 30,000 mCherry- GFP+ cells were sorted from Tg (kdrl:mCherry/runx1:enGFP) at 36 hpf. For STRT-seq in zebrafish, single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry- hematopoietic cells were sorted from the trunk region of Tg (spi2: Gal4;UAS:GFP/ kdrl:mCherry) at 36 hpf. For scRNA-seq of spi2 morphants at 36 hpf in zebrafish, ECs (kdrl+runx1-), HECs (kdrl+runx1+) and hematopoietic cells (kdrl-runx1+) were sorted. For bulk CUT&TAG in zebrafish, fli1a-flag-spi2-EGFP+ cells were sorted from the trunk region of Tg (fli1a-flag-spi2-GFP) embryos at 36 hpf. For 10x Genomics-based scRNA-seq and scATAC-seq in zebrafish, we loaded ~20,000 cells for further 10x Genomics-based scRNA-seq and ~90,000 cells for further 10x Genomics-based scATAC-seq. For scRNA-seq, libraries were prepared using Single Cell 3' Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For ATAC-seq, nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit, and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired-end reads. For 10x Genomics-based scRNA-seq in mice, libraries were prepared using Single Cell 3' Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For STRT-seq in zebrafish, the end-repair and dA-tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. After the adaptor ligation step, the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired-end reads. For bulk cell RNA-seq, libraries were prepared according to STRT-seq method and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired-end reads.