Unit on Cell Specification and Differentiation
Farrell Lab @ NICHD

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Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

In this work, we performed a single-cell RNAseq timecourse of early zebrafish embryogenesis (38,731 cells, across 12 timepoints spanning 3.3 – 12 hours post-fertilization), and reconstructed a branching specification tree leading to 25 cell types.

Browsing the data

  1. Browse the data interactively online in the Broad Single-cell Portal). This allows plotting the expression of genes of interest on the 3D force-directed layout, tSNE projection, or spatially assigned 50% epiboly cells.

  2. Download and install URD, then download the zebrafish data as a pre-processed URD object (requires logging into the Broad Single-cell Portal). This allows more responsive plotting on the 3D force-directed layout, the dendrogram layout, or the tSNE projections (including dual-color plotting of multiple genes), as well as isolation of particular cell populations, differential expression, and more.

Getting the data

  1. The processed genes x cells counts matrix (requires logging into the Broad Single-cell Portal) can be used as a starting point for your own analysis.

  2. Alternatively, the aligned BAM files are deposited in NCBI GEO under accession number GSE106587 along with instructions about downloading and realigning them.