Analysis code and additional data associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'

<p>This dataset is associated with the research manuscript entitled &lsquo;<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>&rsquo; (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The folder &lsquo;<strong>Zenodo_Saxena_etal_2021_AdditionalData_AnalysisCode</strong>&rsquo; contains:</p> <p>&gt; Analysis code used for jerboas-mouse differential RNASeq analysis (<strong>saxena_Interspecies_DESEQ2_analysis.R</strong>).</p> <p>&gt; A folder <strong>Mus_Jac_gtfDir</strong> with two gtf annotation files for 1:1 orthologs in Mouse (musAnno4_1To1Orthologs) and Jerboa (jerboaAnno4_1To1Orthologs) genomes generated with CESAR. This folder also contains two files with mouse or jerboa gene lengths in non-overlapping exons of each gene in the 1:1 orthologous GTF annotations (suffixed &quot;*_exon_lengths_per_gene.txt&quot;). A supporting R library required to run the analysis is provided in this folder (saxena_shared_library_v2.R).</p> <p>&gt;A <strong>STAR_countsDir</strong> folder with STAR generated GeneCounts for mouse and jerboa samples (suffixed &quot;*_SR50&quot;). Subfolders contain metatarsal (MT) and Radius/ulna (RU) STAR Genecounts used in the primary (&ldquo;*_n=3&quot;) and independent validation (&quot;*_n=2&quot;) analyses.</p> <p>&gt; A pdf file with <strong>Additional Figures 1 and 2</strong>. Fig 1 shows RNAScope <em>in situs </em>for <em>Galnt17</em> in jerboa and mouse postnatal day 5 cartilages. Fig 2 shows DESeq2 generated MA-plot for jerboa-mouse metatarsal comparisons (n=3).</p> <p>&gt; <strong>Additional Data Tables_1to3</strong> with DESeq2 differential expression results for all of the 17,464 mouse and jerboa orthologs in the primary (n=3, Table1) and independent validation (n=2, Table2) analyses. r-log&nbsp; transformed gene counts for 17,464 mouse and jerboa 1:1 orthologs in metatarsal samples (n=3, Table3).</p>