Data repository for "Convergent redeployment of ancestral programs during the evolution of mammalian flight membranes"

This repository contains data files and code related to the publication tentatively titled "Convergent redeployment of ancestral programs during the evolution of mammalian flight membranes" by Feigin et al. of the Mallarino Lab at Princeton.

1) PetGlider_PUasm1.0_preNCBI.fasta.gz: Draft genome assembly of the pet-trade glider, an Australasian marsupial commonly referred to as the sugar glider and historically classified as Petaurus breviceps (though the currently taxonomy is disputed). 

2) PetGlider_PUasm1.0_gene_annotations.gff.gz: Gene annotations for the glider assembly generated using the Maker2 pipeline.

3) Ajam_vs_Cper_d4.gff.gz: Gene annotations for Seba's short-tailed bat (Carollia perspicillata). These annotations were generated by lifting over gene models from the related Jamaican fruit bat (Artibeus jamaicensis; WHU_Ajam_v2 available on NCBI at https://www.ncbi.nlm.nih.gov/genome/?term=Artibeus+jamaicensis) to the Seba's short-tailed bat assembly produced by DNAZoo (https://www.dnazoo.org/assemblies/Carollia_perspicillata) using the program liftoff.

4) WGCNA_sample_prep.r: Code used to prepare sugar glider RNA-Seq read counts for subsequent analysis with WGCNA

5) pat_network_construction_WGCNA.r: Code used to perform network construction of sugar glider RNA-Seq read count data across development with WGCNA.

6) sugar_glider_pat_vs_shd_vs_dors.r: Code used to perform differential gene expression analyses comparing sugar glider patagium skin RNA-Seq data to that of shoulder and dorsal skin regions.

7) bat_pat_vs_dors.r: Code used to perform differential gene expression analyses comparing Seba's short-tailed bat plagiopatagium skin RNA-Seq data to that of dorsal skin.

Scripts from this project can also be found at: https://github.com/charlesfeigin/Petaurus-glider-transcriptomics-code