Ascidian embryonic cells with properties of neural-crest cells and neuromesodermal progenitors of vertebrates

Expression matrices used for a cross-species comparison between zebrafish and Ciona transcriptomes, and R-markdowns for analyzes using Seurat.

Single-cell transcriptome data for Ciona middle gastrula embryos to larvae, which were published previously (Cao, C. et al. 2019 Nature 571, 349-354. doi: 10.1038/s41586-019-1385-y), were used (SRA accession numbers: SRR9050988, SRR9050989, SRR9050992, SRR9050997, SRR9050998, SRR9051003, and SRR9051007). Data were mapped to the latest genome assembly (HT version) (Satou, Y. et al. 2019. Genome biology and evolution 11, 3144-3157. doi:10.1093/gbe/evz228) and the latest version of the gene model set (KY21 version) (Satou, Y. et al. 2022. Zool Sci 39, 253-260. doi: 10.2108/zs210102) using Cell Ranger software (version 6.12. 10xGenomics). For zebrafish 10- to 24-hr embryos, mapping data to gene models were downloaded from the GEO database (we used CSV files of UMI-filtered counts under accession numbers, GSM3067192 to GSM3067195; GSM3067192_10hpf.csv.gz, GSM3067193_14hpf.csv.gz, GSM3067194_18hpf.csv.gz, and GSM3067195_24hpf.csv.gz) (Wagner, D. E. et al. 2018. Science 360, 981-987. doi: 10.1126/science.aar4362). For comparisons between Ciona and zebrafish transcriptomes, we first compared proteomes of Ciona and zebrafish using OrthoFinder (Emms, D. M. & Kelly, S. 2015. Genome Biology 16. doi: 10.1186/s13059-015-0721-2). When multiple genes for one species were included in one ortholog group, all read counts in that group were summed in the expression matrices.

Data S1. The expression matrix for zebrafish embryos.

Data S2. The expression matrix for ascidian middle gastrula embryos. 

Data S3. The expression matrix for ascidian early neurula embryos. 

Data S4. The expression matrix for ascidian late neurula embryos. 

Data S5. The expression matrix for ascidian middle tailbud embryos (replica 1). 

Data S6. The expression matrix for ascidian middle tailbud embryos (replica 2). 

Data S7. The expression matrix for ascidian late tailbud embryos. 

Data S8. The expression matrix for ascidian larvae. 

Data S9. The R-markdown for a comparison of gene expression profiles among Ciona larval tissues.

Data S10. The R-markdown for a cross-species comparison between Ciona transcriptomes and zebrafish transcriptomes.