Processed data from scRNA-seq protocol conducted throughout the Oikopleura dioica lifecycle

We used Cellranger (https://github.com/10XGenomics/cellranger) to processe single-cell RNA sequencing reads produced from Oikopleura dioica samples collected at successive developmental stages (2 to 16 hours post-hatching, then 5 to 7 days post-hatching). For each developmental stage, Cellranger output includes cell barcodes, count matrices and genes. We used Seurat (https://satijalab.org/seurat/) to normalize the filtered data, and to conduct principal component analysis. Clustering of cell types was conducted after batch correction with the Harmony package (https://github.com/immunogenomics/harmony). We provide a collection of Seurat objects produced by the clustering of either individual developmental stages, combined adult stages only, adult cellulose-producing cells only, and aggregated data from all samples. We also provide Seurat objects produced by processing scRNA-seq data produced by Cao et al. with Ciona intestinalis (DOI: 10.1038/s41586-019-1385-y ).