Contents

Data and scripts of "Natural variation in copper tolerance in Drosophila melanogaster is shaped by transcriptional and physiological changes in the gut" (Green et al. 2021).

Differential gene expression analyses

1. DE_analysis.R: R script for performing DE analyses, GO enrichment and visualizations
2. DESeq2-input folder: sample_sheet_*.txt contain the table of sample information for DESeq2
3. DESeq2-input folder: counts_*.txt are the raw gene counts

Linear model analyses

1. analysisLM.Rmd: Rmarkdown for performing the multiple linear regression model
2. dataLM.tab data for performing the multiple linear regression model

Kaplan-Meier analyses

1. Kaplan-Meier folder: data_to_kaplan.pl script to create input for survival analysis. File example.tab is the input and example_outputKM.tab is the output.
2. Kaplan-Meier folder: survival.R R script to analyse mortality data using output of data_to_kaplan.pl as input (Kaplan-Meier plots and log rank test in R)

Gut acidity and feeding analyses

Scripts and data to perform the chi-squares, post-hoc tests and t-test. Data to reproduce Figure 5.

Reference

Green et al., (2021) The genomic basis of copper tolerance in Drosophila is shaped by a complex interplay of regulatory and environmental factors (BioRxiv).