Neural crest lineage in the proto-vertebrate model Ciona

Larva single cell data (SRA accession number: SRR9051005, SRR9051006 and SRR9051007) from Cao and colleagues (GEO accession number: GSE131155; Cao et al, 2019)  were remapped on the Ciona KY21 gene models released in 2022 (Satou et al, 2019; Satou et al, 2022) using CellRanger v7.0.0. The expression matrices were analyzed with the package Seurat v4.3.0 (Butler et al, 2019) in R version 4.2.3 (R, 2022). The different tissue types were first identified (Table1_tissueTypes-wholeLarvae) before the nervous system was subsetted and the neural cell types identified (Table2_cellTypes-nervousSystem). The significantly differentially expressed genes between the Hh2+ ependymal cells (Table3_DEGs) and the rest of the nervous system were identified with Seurat using Wilcoxon rank-sum test with Bonferroni correction (Butler et al, 2019).