Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes

<p>Dataset used to reproduce the analysis performed in &quot;Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes&quot; publication. The directory structure is the following:</p> <ul> <li>Gene_models - directory containing gene models (.gtf or .gff3 files) used for feature length comparisons across species</li> <li>intermediate_data - directory containing intermediate results from various scripts, the main purpose is to speed up the reproducibility of some longer running scripts <ul> <li>batch_adjusted_normalised_gene_expression_matrix.tsv - gene expression matrix used for evolutionary model fitting</li> <li>fc.tsv - fold change matrix used for evolutionary model fitting</li> <li>dated_species_tree.tre - species tree used throughout the model fitting step (newick format)</li> <li>DGE_script_enviorment.RData - saved R environment from differential gene expression analysis</li> <li>downregulated_IDs.RDS - gene IDs which undergo down-regulation throughout maternal-to-zygotic transition</li> <li>maternal_IDs.RDS - gene IDs which meet the cut-off criteria for being considered as maternally expressed</li> <li>N0_blasted.tsv - orthogroup annotations through blasting to a sequence database</li> <li>N0.tsv - orthogroups inferred from OrthoFinder</li> <li>OG_categories.tsv - classification of orthogroups based on them (I) having genes with maternal expression, but no significant down regulation, (II) having genes with maternal expression and significant down regulation throughout maternal-to-zygotic transition or (III) no maternal expression</li> <li>OG_presence.tsv - binary matrix coding for which orthogroup which species have gene expression values</li> <li>Paralog_variances.tsv - matrix containing variance metrics for paralogs in each species from before normalization across species</li> </ul> </li> <li>Pannzer2_annotation - directory containing GO annotations for all species from the Pannzer2 tool, used for GO analyses</li> <li>quantification_files - directory containing all salmon quantification outputs</li> <li>transcriptomes - <em>de novo</em> assembled transcriptomes for non-model species</li> </ul>