Joint single-cell RNA and ATAC sequencing Atlas

As a continuation of our single cell transcriptomic atlas, we performed single-cell Multiome assay (10xGenomics), jointly profiling single-cell RNA-seq and ATAC-seq, for each of six developmental stages - bud stage, 5-, 10-, 15-, 20-, and 30-somites, resulting in a time-resolved, single-cell multi-omic atlas of 94,560 cells. Like in our initial release, our goal is to provide both high quality single-cell RNA and ATAC sequencing time-resolved data that allows for a more in-depth exploration and understanding of zebrafish development.

By coupling chromatin accessibility and gene expression, we gain a comprehensive understanding of the dynamics between open regions of DNA and the corresponding RNA being expressed for tens of thousands of genes across developmental stages. We also build time-resolved gene regulatory networks, GRNs, for each cell type, as well as performing in silico genetic perturbation (with the power of CellOracle) to simulate the cell fate transitions.

Modalities

We generated UMAPs in transcriptomic, epigenomic, and joint space, allowing for the selection of particular developmental stages and cell types. Cell type annotation was performed by transferring labels from our previous expert annotations using the RNA modality.

Interactive Figures

To make the most out of our dataset, we provide interactive figures for the exploration of your favorite gene or developmental stage. Click below to see how gene activity and expression correlate over time, how genes and transcription factors interact, and to see the effect of in-silico knockouts. For now we provide these capabilities for neural-mesoderm progenitors (NMPs) and corresponding trajectories, however, whole embryo gene regulatory networks and knockouts will be available soon!

The main citation for our epigenomics datasets is:
Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis

You can find the list of all Zebrahub-related papers here.