Scripts and data on Wnt signalling, cell fate determination and anteroposterior polarity of the skate gill arch skeleton

<strong>Scripts:</strong> Scripts S.3.1–S.3.4 detail bash script containing the code used to assemble the Leucoraja erinacea GAER transcriptome. Includes: - Script S.3.1: Initial quality check on raw data. - Script S.3.2: Recleaning of data to include only 149-150bp reads. - Script S.3.3: Normalisation of data pre-assembly. - Script S.3.4: Trinity assembly. <br> Scripts S.3.5–S.3.7 detail bash script containing the code used to check my assembled transcriptome. Includes: - Script S.3.5: Assessing RNA-Seq read representation. - Script S.3.6: Assessing representation of full length reconstructed protein coding genes by searching the assembled transcripts against Uniprot. Includes counting full length transcripts and examining the percent of the target being aligned to by the best matching Trinity transcript. - Script S.3.7: Calculating the transcript abundance estimation. <br> Scripts S.3.8–S.3.10 contain the code used for differential expression analysis and analysing genes of interest. Includes: - Script S.3.8: Bash script calculating the transcript abundance estimation to generate a salmon gene counts matrix file removing two libraries. - Script S.3.9: Bash script for extracting fasta sequences of highest expressed isoforms. - Script S.3.10.Rmd: R file detailing differential gene expression analysis and generation of volcano plots. <br> <strong>Tables:</strong> - Table S.3.1: <em>Leucoraja erinacea</em> genes differentially expressed in GAER vs control tissue manually annotated with gene names. - Table S.3.2: <em>Leucoraja erinacea</em> genes differentially expressed in GAER vs control tissue annotated with colour labelling for volcano plot. - Table S.3.3: Raw data of Salmon gene counts matrix. - Table S.3.4: Salmon gene expression matrix. - Table S.3.5: Assembly statistics. <strong>Figures:</strong> - Fig. S.3.1: Graphs showing biological coefficient of variation, mean difference plot and multidimentional scaling plots pre and post-batch effect.