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 Dashboards

To make the most out of our dataset, we provide interactive dashboards for the exploration of your favorite gene or developmental stage. Click below to see how gene accessibility and activity change over time, how accessible regions of the genome correspond to different regulatory programs, and how genes and transcription factors interact.

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.