Supporting Data for thesis 'Cell Type Diversity During Sea Urchin Development: A Single Cell Approach to Reveal Different Neuronal Types and Their Evolution'

The non-book component contains supplementary data to support Chapters 3, 4, and 5.
Moreover, the thesis abstract is attached.Abstract.docx
Files containing the code (R Scripts) used to run the analyses:Subclustering analysis.rmd (subclustering analysis of neuronal, skeletal, immune and apical plate cell types)Sp_2dpf_clustering analysis.rmd (clustering analysis of the 2 dpf scRNA-seq dataset)Sp_3dpf_clustering analysis.rmd (clustering analysis of the 3 dpf scRNA-seq dataset)Sp_5dpf_clustering analysis.rmd (clustering analysis of the 5 dpf scRNA-seq dataset)Sp_2_3_dpf_clustering analysis.rmd (clustering analysis of the 2 and 3 dpf integrated scRNA-seq datasets)
Data discussed in Chapter 3 "Embryonic and larval cell types at a single cell resolution"
1.Tables containing all the S. purpuratus genes expressed in different time-points and cell types. The average expression and the average scaled expression is reported. Annotated by WHL ID.Sp_2dpf_all_genes.xlsxSp_3dpf_all_genes.xlsSp_5dpf_all_genes.xlsx
2.Tables containing all the S. purpuratus marker genes (highly differentially expressed genes) in different time-points and cell types. P_value and adjusted P_value are reported. Annotated by WHL ID.Sp_2dpf_marker_genes.xlsSp_3dpf_marker_genes.xlsSp_5dpf_marker_genes.xls
3.Table containing additional information on the genes identified in this thesis (NCBI annotation, go annotation, PFAM).Sp_genes_annotation_NCBI_GO_PFAM_FUNCTIONAL.xls
Data discussed in Chapter 4 "Neuronal diversity during sea urchin development"
1.Table containing all the S. purpuratus genes expressed in different neuronal types of the 3dpf pluteus larva. The average expression and the average scaled expression is reported. Annotated by WHL ID.
Sp_3 dpf neuronal subclustering_all genes

Data discussed in Chapter 5 "Pancreatic-like cell types in sea urchin"
1.Tables containing all the S. purpuratus affected genes after Sp-Pdx1 knockdown at 3dpf pluteus larva and the ones affected only in the PPE neurons. (wild type condition vs. Sp-Pdx1 knockdown larvae at 3 dpf). Annotated by WHL ID.
Sp-Pdx1 differential RNA-seq.xlsxDifferentially expressed genes in the PPE neurons.xls