This dataset is associated with the research manuscript entitled ‘Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion’ (https://www.biorxiv.org/content/10.1101/754002v2). The folder ‘Zenodo_Saxena_etal_2021_AdditionalData_AnalysisCode’ contains: > Analysis code used for jerboas-mouse differential RNASeq analysis (saxena_Interspecies_DESEQ2_analysis.R). > A folder Mus_Jac_gtfDir 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 "*_exon_lengths_per_gene.txt"). A supporting R library required to run the analysis is provided in this folder (saxena_shared_library_v2.R). >A STAR_countsDir folder with STAR generated GeneCounts for mouse and jerboa samples (suffixed "*_SR50"). Subfolders contain metatarsal (MT) and Radius/ulna (RU) STAR Genecounts used in the primary (“*_n=3") and independent validation ("*_n=2") analyses. > A pdf file with Additional Figures 1 and 2. Fig 1 shows RNAScope in situs for Galnt17 in jerboa and mouse postnatal day 5 cartilages. Fig 2 shows DESeq2 generated MA-plot for jerboa-mouse metatarsal comparisons (n=3). > Additional Data Tables_1to3 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 transformed gene counts for 17,464 mouse and jerboa 1:1 orthologs in metatarsal samples (n=3, Table3).