Rabbit_Domestication_Brain_RNA_Seq

IN this repository you find codes for analysis of RNA-seq data generated from four brain parts published in ......

Codes and data

All the scripts used to analyze data and make tables & figures are stored in /Codes/ directory. Raw data are available from Supplementary Database S4-6, which are supposed to be stored in /Data/raw_data/ directory in the instructions below.

Deposited raw data

All_dAF_0.5over : All the SNP coordinates with dAF above 0.5.

All-Sweeps.bed : The regions with signature of selective sweep in domestic rabbits, which can be found as Database_S1 in the paper of Carneiro et al. 2014 Science.

Deltas_vs_OryCun2.liftover.29mCons.mapped.chrUnFixed.sorted.DeltasOver0.8.bed_NOT_ANY_OTHER_EXON.bed : The SNPs with dAF above 0.8 located in highly conserved non-coding regions.

Dopamine_Ciliary_genes.tsv : The list of genes relevant to dopamine or ciliary functions detected in DE analyses.

Ens76~ or Oryctolagus_cuniculus.OryCun2.0.76.gtf: Reference information downloaded from Ensembl ver.76.

Ribosomal_Proteins.tsv : The list of genes coding ribosomal proteins.

Normalization of count data

run_TMM_scale_matrix.pl : The Perl script to normalize the count data by TMM implemented in edgeR, downloaded from trinity. This can be run as follows.

perl run_TMM_scale_matrix.pl --matrix Brain-R7-9-Ami-Hyp-count-s-3 > Brain-R7-9-Ami-Hyp-count-s-3_TMM_FPKM.matrix

This step has been already conducted and the normalized count data are available from Database S4.

Differential expression analysis

DEanalysis.R: Conduct the DE analysis for each brain region with exactTest. Genes with CPM < 1 for three or more samples in a comparison were excluded. Differentially expressed genes (DEGs) were evaluated under three thresholds: 1) FDR < 0.01, 2) |Log2FC| > 1 and 3) SD/Mean of CPM in a group < 1 and no overlaps in CPM between (domestic and wild) groups.

DatabaseS2.R: Conduct the DE analysis for each brain region under different labeling set of wild and domestic.

Gene enrichment analysis

DAVID (v.6.8): https://david.ncifcrf.gov

GREAT (v.4.0.4): http://great.stanford.edu/public/html/

PPI network analysis

STRING (v.11.0): https://string-db.org

• Download the resultant network file as tsv.

Cytoscape (v.3.8.0): Settings of MCODE are as below.

• Uncheck "include loops"
• Degree Cutoff: 5
• "Fluff" and "Haircut"
• Node Density Cutoff: 0.7
• Node Score Cutoff: 0.7
• K-Core: 3
• Max. Depth: 100

Tables and figures

You can reproduce all the results by running the given scripts corresponding to each analysis.