Amphioxus neurula cell atlas

In this interactive database you will be able to access and explore our single-cell transcriptomic atlas of the neurula of Branchiostoma lanceolatum, the Mediterranean amphioxus. You can read more about it in our preprint: “An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm” (Grau-Bové, Subirana et al., bioRxiv 2023).

Here you can browse four datasets: the whole-embryo dataset (neurula stage, 21 hours post-fertilisation) and three sub-set analyses corresponding to the endoderm, somites, and neural cells.

How to use this database

For each of the four datasets, we cluster and annotate cells at two levels: as metacells (transcriptionally coherent clusters of cells with high granularity), and cell types (groups of metacells).

You can explore gene expression in these cell clusters from different perspectives. First, select your dataset of interest and click on Generate cell atlas. Then, you can explore four pages:

1) Overview – This will show the metacells and single-cells arranged on a 2D projection, with cell type labels, as well as a heatmap showing expression of variable genes. Here you can also download the metacell gene expression matrix (fold-change values) and the raw single-cell UMI counts matrix.

2) Single gene query – Show gene expression for an individual gene. You can select the gene based on gene ID (e.g. BLAG14000136), gene name (e.g. MYO16), or Pfam domain (e.g. “Myosin_head” will give you all the genes with a myosin domain, for you to select from). You can also launch a BLAST search with your protein of interest, and select a gene from there.

3) Multiple genes query – This allows the visualization of multiple genes at once. You can search genes by name, annotation, or Pfam domain and you can also upload a list of interest. We also provide predefined lists of genes for different families/sets of function (e.g. transcription factors).

4) Cell type markers – This will give you a list of genes specific to a certain cell type, metacell, or group of metacells of your choice. First you need to select the metacells or a cell types of interest. Then, you need to select an expression threshold for marker selection (fold change). Optionally, you can request that the gene is expressed in all other metacells below a certain threshold. This generates a table of the top marker genes fulfilling the selected criteria. You can sort them using different metrics and also specifically select transcription factors. This table can be downloaded.