##### README for Datafiles Accompanying Everman et al. 2020

# DSPR_Data/:

Adult_Copper_Resistance.txt

Tab-separated txt file of adult copper resistance reported in percent survival for each strain with summary statistics. 
Data are presented in Figure 1, Figure 2, Figure 4, Figure S3.
Column headers:
	Strain = Recombinant Inbred Line ID from the DSPR
	Subpop = Subpopulation of the DSPR
	Sex = Female
	N = Number of vial replicates
	Survival = Percent survival after 48 hours, averaged across replicates
	SD = Standard deviation
	SE = Standard error
	CI = 95% confidence interval


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Adult_Feeding_Response.txt

Tab-separated txt file of raw absorbance readings and estimated percent dye consumed for each vial replicate.
Data are presented in Figure 2.
Column headers:
	Plate = Plate ID
	Position = Well position in plate
	Sex = Female
	Treatment = Control or Copper (50mM)
	Block = Block of experiment
	Date.Read = Date absorbance readings for the plate were taken
	Absorbance = Absorbance at 600nm
	PercentDye = Estimated percent dye consumed determined from standard curve calculation


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Standard_Curve.txt

Tab-separated txt file of standard curve absorbance readings.
Data are presented in Table S1.
Column headers:
	Plate = Plate ID
	Position = Well position in plate
	Standard.DyeConcentration = Concentration of dye (%) in each standard
	Block = Block of experiment
	Date.Read = Date absorbance readings for the plate were taken
	Absorbance = Absorbance at 600nm	
	
	
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Developmental_Response.txt

Tab-separated txt file of average development time and developmental viability.
Data are presented in Figure 3, Figure 4, Figure S2.
Column headers:
	Trait = Viability (Square root transform) or Days to Emergence
	Strain = Recombinant Inbred Line ID from the DSPR
	Control = Average response under control conditions (% viability or days)
	Copper = Average response under copper conditions (% viability or days)
	Copper-specific.Response = Copper-specific developmental viability or copper-specific development time (residuals)
	
	
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LODscores.txt

Tab-separated txt file of DSPR LOD score from QTL mapping analyses.
Data are presented in Figure 5.
Column headers:
	Trait = Adult Copper Resistance, Copper-specific Dev. Viability, Copper-specific Dev. Time
	Panel = DSPR panel
	Sex = Female
	chr = Chromosome (X, 2L, 2R, 3L, 3R)
	Ppos = Position on chromosome based on assembly 5.0
	Gpos = Genetic position
	LOD = LOD score from QTL mapping analysis
	
	
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Corrected_LODscores.txt

Tab-separated txt file of DSPR LOD score from QTL mapping analyses corrected for block and after excluding vials with fewer than 15 flies.
Data are presented in Figure S4.
Column headers:
	Correction = Factor taken into consideration for the model: Block or excluding vials with fewer than 15 flies (> 15 Flies)
	Panel = DSPR panel
	Sex = Female
	chr = Chromosome (X, 2L, 2R, 3L, 3R)
	Ppos = Position on chromosome based on assembly 5.0
	Gpos = Genetic position
	LOD = LOD score from QTL mapping analysis


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QTLPeaks.txt

Tab-separated txt file of peaks from QTL mapping analyses for adult copper resistance and copper-specific developmental viability.
Data are presented in Figure 6, Figure S6.
Column headers:
	Trait = Adult copper resistance or copper-specific developmental viability
	Panel = DSPR panel
	QTL = QTL identified from mapping analyses
	Founder.Haplotype = Founder haplotype strain
	Estimate = Estimated effect of each founder haplotype on adult copper resistance and copper-specific developmental viability
	SE = Standard error of the estimated effect of each founder haplotype


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NormalizedTPM.txt

Tab-separated txt file with quantile-normalized TPM data prior to additional filtering out of genes with less than 1 TPM and expression variance greater than 1.
Data were filtered and used to run Clust analysis for treatment and resistance class genes with differential expression
Column headers:
	gene.name = Name of gene
	C_21037_S3..Cu_22460_S16 = Sample IDs. C = Control, Cu = Copper; 2XXXX = DSPR Strain ID; S1..S20 = Sample number
	

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NormalizedTPM_Treatment.txt

Tab-separated txt file with quantile-normalized TPM data for genes with differential expression due to Treatment after additional filtering out of genes with less than 1 TPM and expression variance greater than 1.
Data is the input file used to run Clust analysis for treatment
Column headers:
	gene.name = Name of gene
	C_21037_S3..Cu_22460_S16 = Sample IDs. C = Control, Cu = Copper; 2XXXX = DSPR Strain ID; S1..S20 = Sample number


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NormalizedTPM_Resistance.txt

Tab-separated txt file with quantile-normalized TPM data for genes with differential expression due to Resistance Class after additional filtering out of genes with less than 1 TPM and expression variance greater than 1.
Data is the input file used to run Clust analysis for resistance class
Column headers:
	gene.name = Name of gene
	C_21037_S3..Cu_22460_S16 = Sample IDs. C = Control, Cu = Copper; 2XXXX = DSPR Strain ID; S1..S20 = Sample number


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PCA.txt

Tab-separated txt file with data from Principal Components Analysis of gene expression for 1589 differentially expressed genes from the full model analysis.
Data are presented in Figure 7, Figure 9.
Column headers:
	Resistance.Class = High or Low resistance, based on adult copper resistance
	Treatment = Control or Copper
	Strain = Recombinant Inbred Line ID from the DSPR
	PC1..PC20 = principal components loadings
	
	
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Gene_Induction.txt

Tab-separated txt file of gene induction by copper for all genes.
Data are presented in Figure 8, Figure S7.
Column headers:
	Gene = Gene name
	Resistance = High or Low resistance, based on adult copper resistance
	FullModel.SignificantGenes = Significantly differentially expressed genes identified with the full model
	TreatmentModel.SignificantGenes = Significantly differentially expressed genes identified with the treatment model
	ResistanceModel.SignificantGenes = Significantly differentially expressed genes identified with the resistance model
	Gene.Induction = Change in gene expression as a result of copper exposure relative to control expression
	
	
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RNAi.AvgLifespan.txt

Tab-separated txt file of average lifespan of TRiP UAS RNAi knockdown strains.
Data are presented in Figure 10.
Column headers:
	BDSC.ID = Bloomington Drosophila Stock Center ID number
	Batch = Batch of experiment
	Tissue = Tissue where gene was knocked down (WholeAnimal vs. Anterior Midgut)
	N = Number of flies per vial
	Sex = Female
	AvgLifespan = Average Lifespan (hours) of flies in each vial
	Gene = Gene knocked down
	
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# DGRP_Data/EggCountImages/:	
	Contains pictures of eggs for the developmental assays.
	File naming scheme: 2XXXX_Date.JPG = DSPRSTRAIN_DATEOFASSAY.JPG