README: Neuronal function and dopamine signaling evolve at high temperature in Drosophila

https://doi.org/10.5061/dryad.6m905qg62

This dataset contains RNA-seq read count and differential expression data, Drosophila behaviour data (spontaneous activity and startle-induced negative geotaxis after cocaine and 3IY treatment), powdered D. melanogaster and melanin FTIR-spectra and associated custom scripts and support files used to produce final results of this study.

Description of the data and file structure

RNA-seq
-> RNAseq_counts.txt contains a tab delimited text file including raw RNA-seq read counts for all samples (columns) and genes (rows)
-> RNA-seq_countLabels.xls is an excel file containing an explanation of labels (column names) of the read count table and the mapping of label abbreviations to the original replicate name designation
-> temperaturefx.txt is a tab delimited text file containing log2 fold-change (logFC), log2 counts per million (logCPM), p-value (PValue) and FDR correction of p-value using Benjamini-Hochberg method (FDR) for the following pairwise population comparisons: Ancestral versus Cold evolved (BC), Ancestral versus Hot evolved (BH), Hot versus Cold evolved (HC), Evolved versus Ancestral (LB, "Laboratory adaptation").

->fbgn2fbbt.tsv file is a tissue expression annotation file

->active_zone_genes is a list of gene names used in the differential gene expression analysis

->neurotransporter_genes is a list of gene names used in the differential gene expression analysis

Spontaneous locomotor activity
-> standard output files from Drosophila Activity Monitor System

-> columns represent individual flies of the indicated genotype

-> rows are time steps at which activity (number of times the fly passed the middle of the tube) was recorded

mon_27-28-30.11_01-05.12.txt - Spontaneous locomotion for evolved and ancestral replicates (column names are unique fly identifiers and indicate selection line (B -> base (ancestral) flies, C -> cold evolved flies, H -> hot evolved flies), replicate, and a fly id that is unique within the evolved replicate. Flies with no id number are assigned with id number 0. (E.g. "C1.1" is cold evolved replicate one, fly 1 or "H2" is hot evolved replicate 2, fly 0)

mon_27-28-30.11_01-05.12_names.txt - Spontaneous locomotion for evolved and ancestral replicates. This is the same file as mon_27-28-30.11_01-05.12.txt but instead fly id the column names have information of the day (date) when the activity was measured. Dates range from 27th Nov to 5th Dec, and are coded as DD_MM. Fly id is unique only within a given day. Column names are unique fly identifiers.

mon_DA_deficient_mutant.txt - Spontaneous locomotion for dopamine deficient mutant line

mon_DA_shRNAi.txt - Spontaneous locomotion for short hairpin RNAi knockdown lines

mon_ddc_all.txt -- Spontaneous locomotion for short ddc>GAL4xRNAi knockdown lines

mon_elav_all.txt -- Spontaneous locomotion for short elav>GAL4xRNAi knockdown lines

mon_mef2_all.txt -- Spontaneous locomotion for short mef2>GAL4xRNAi knockdown lines

FTIR spectra

-> csv files containing wavenumber and absorbance for powdered Drosophila samples from evolved replicates (sim_base/cold/hot), yellow mutant flies with no pigmentation, pure melanin samples, and powdered Drosophila samples with a pure melanin spike-in

fl_sim_base_b2_males.csv

fl_sim_base_b3_males.csv

fl_sim_base_b4_males.csv

fl_sim_cold_11_males.csv

fl_sim_cold_14_males.csv

fl_sim_cold_17_males.csv

fl_sim_cold_19_males.csv

fl_sim_cold_20_males.csv

fl_sim_hot_01_males.csv

fl_sim_hot_02_males.csv

fl_sim_hot_05_males.csv

fl_sim_hot_06_males.csv

fl_sim_hot_07_males.csv

fl_sim_hot_08_males.csv

fl_sim_hot_09_males.csv

fl_sim_hot_10_males.csv

males_2_1_melanin_spikein_spectra.txt

males_all_duplicate_spectra.txt

melanin_pure_as_obtained.csv

yellow_mutant_f1_r3_males.csv

yellow_mutant_spectra.txt

yellow_mutants_males.csv

Startle response
-> all tab-delimited text files contain readings of position of each fly in the 100mL graduated cylinder
-> each of the 54 rows of the file (except the header with column names) represents each mark of the cylinder
-> the values are counts of flies that reached the height corresponding to the area between the mark and the mark just below 30 seconds after being tapped on the floor
-> first row designates the area between the floor and the lowest mark on the cylinder, i.e. all the flies that either stayed on the floor or did not pass the lowest achieved height
-> value 200 designates no fly was reached above this height (200 is used for an easy conversion to NA during data analysis)
-> the hot evolved replicates are designated with Hxx, cold evolved with Cxx and ancestral with Bxx where "xx" is the replicate number
-> cocaine-treated replicates are marked with yyy_coc, 3IY-treated flies with yyy_3iy and vehicle treated flies with yyy_con, where 'yyy' designates the population replicate

startle_28C_2018_06_04_3IY_2ul_30sec.txt

startle_28C_2018_06_11_cocaine_2ul_30sec_1.txt

startle_28C_2018_06_11_cocaine_2ul_30sec_2.txt

startle_28C_2018_06_12_3IY_2ul_30sec_1.txt

startle_28C_2018_06_12_3IY_2ul_30sec_2.txt

Scripts

-> .r files containing scripts used to obtain main results in the manuscripts (R version has not been logged but based on release dates likely R 3.4.0-3)

-> in some scripts where spontaneous locomotion was analysed and aggregated over 10 minute steps, raw activity monitor files named "Monitor1-5.txt" are indicated as input files. Those files in fact correspond to spontaneous locomotor activity data uploaded here, so that data from all monitors that were ran in parallel are combined in one single activity file. The colum names in these files correspond to the genotype and unique, individual flies, so that they can be easily extracted from the main file and analysed independently if needed

DA_deficient_plot.r

• R-script used to visualise spontaneous locomotion of DA deficient mutant line and shRNAi knockdown
• uses mon_DA_deficient_mutant.txt and mon_DA_shRNAi.txt as data input
• libraries used are pracma and fields (version has not been logged, but based on the release dates last versions available in 2017)

cocaine_3IY.r

• R script used to format, analyse and visualise startle response data
• uses startle_28C_2018_06_11_cocaine_2ul_30sec_1.txt, startle_28C_2018_06_11_cocaine_2ul_30sec_2.txt and startle_cocaine_28C_2018_05_11.txt as data input
• libraries used are lme4 and lsmeans (version has not been logged, but based on the release dates likely lme4 1.1-15 and lsmeans 2.27)

full_RNAi_script.r

• R script used to format, analyse and visualise spontaneous locomotion in gene knockdown experiments
• libraries used are lme4 and lsmeans (version has not been logged, but based on the release dates likely lme4 1.1-15 and lsmeans 2.27)
• data used: mon_elav_all.txt. mon_ddc_all.txt, mon_mef2_all.txt

neurotransporter_genes

• text file with a list of neurotransmitter transporter genes used in neuron_markers.r

active_zone_genes

• text file with a list of genes encoding proteins expressed in the synaptic active zone

fbgn2fbbt.tsv.gz

• Drosophila tissue expression annotation file obtained from fly base, used for tissue enrichment analysis used in final_script.r

mai.r

• R script used to identify melanin-specific absorbance wavelength from cuticle IR spectra
• data used: males_all_duplicate_spectra.txt,males_2_1_melanin_spikein_spectra.txt, yellow_mutant_spectra.txt

final_script.r

• R script used for formatting raw read count data and for differential gene expression analysis.
• data used: monster_fullset_readcounts.csv (RNAseq_counts.txt), fbgn2fbbt.tsv
• libraries used edgeR, gplots, RColorBrewer, ggplot2, matrixStats. Library versions have not been logged but the most likely versions are released in 2017

neuron_markers.r

• R script used to plot expression changes in neutron-type specific genes

• data used: neuron_marker_genes.txt (neurotransporter_genes file)