Single-cell multi-omic dataset mapping chromatin modifications and transcriptome during zebrafish development

Establishing a cell-type-specific chromatin landscape is crucial for the maintenance of cell identity during embryonic development. However, our knowledge of how this landscape is set during vertebrate embryogenesis has been limited, due to the lack of methods to jointly detect chromatin modifications and gene expression in the same cell. In this study, we apply T-ChIC, a method for joint profiling of histone modifications and transcriptome of single cells, to study the early embryonic development in Zebrafish (4-24 hpf). Overall design: Wild-type TL embryos were collected 20 minutes after fertilization in a petri dish with E3 medium and kept at 28.5°C in an incubator. For early time points (4, 6, and 8 hpf), cells were dissociated with FACSmax cell dissociation solution at RT. For later time points (10, 12 and 24 hpf) cells were dissociated Protease solution on a shaker at 28°C and 400 rpm, resuspending vigorously every 2 minutes. Cells were washed and incubated with CellTrace (thermofisher) kit using different colors for each timepoint. They were then pooled in a 0.5-mL protein-low binding tube to end up with approximately 1 million cells in total. They were then processed using the tChIC protocol. The detailed, step-by-step scT-ChIC protocol is available at: https://www.protocols.io/view/single-cell-tchic-for-zebrafish-q26g7pbe8gwz/v1 The data preprocessing pipeline (from .fastq to count tables and peaks) is available at: https://github.com/bhardwaj-lab/scChICflow . The processed data presented here was mapped to the genome version: GRCz11/danRer11, and gene annotations used were Ensembl v104.