Cell state transitions are decoupled from cell division during early embryo development [II]

Paper abstract: As tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation, we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single-cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However, in the absence of cell division, differentiation slows down in some cell types, and cells exhibit global stress responses. While differentiation is robust to blocking cell division, the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo-wide perturbations with single-cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24, 38 and 48 hours post fertilization (hpf) were collected. Cells were dissociated from these tails and multi-seq tags were added to the cells for each time point. Cells from all time points were pooled and single-cell sequencing was performed using Indrops. Four gene expression (GEX) libraries were prepared for transcriptomic information and four multiseq tag libraries (TAG) were prepared for reading out the multiseq tags. We provide the raw data (.fastq files), processed data - both raw (counts.tsv.gz) and filtered by total UMI counts (filtered.h5ad files) and the entire filtered data after removing doublets as all_data.h5ad. We also provide counts for multi-seq tags (example, TAG_1.counts.csv). Information about pooling libraries and library indices is provided in Pooling_Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state information we provide in the all_data.h5ad is only for 24 hpf.