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'

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).