DOI: 10.5281/zenodo.17992787
title: RNA-seq transcriptomic profiles of Aedes aegypti exposed to broflanilide and imidacloprid in two populations

description: This dataset contains gene-level RNA-seq data and differential expression results from Aedes aegypti mosquitoes belonging to two populations (New Orleans reference strain and a field-derived population from San Nicolás, Mexico) exposed to two insecticides with distinct modes of action: broflanilide and imidacloprid. Adult females from each population were exposed to either insecticide or solvent control, and whole-body transcriptomes were sequenced in three biological replicates per strain–treatment combination (18 libraries in total).

Raw read counts were generated with featureCounts using the Aedes aegypti reference genome (AaegL5), and differential expression analyses were performed with DESeq2 contrasting insecticide-exposed versus control groups within each population, as well as population differences under matched exposure conditions. Significantly differentially expressed genes (DEGs) were defined using an adjusted p-value threshold of 0.05 and |log₂ fold change| > 1, and Gene Ontology (GO) enrichment analyses (Biological Process, Cellular Component and Molecular Function) were carried out using NCBI GeneID-to-GO mappings.

The three Excel files provided include: (i) sample metadata and raw/filtered gene counts, (ii) complete DESeq2 results for all pairwise comparisons, and (iii) filtered DEG lists together with GO enrichment tables for Biological Process, Cellular Component and Molecular Function. These data support the associated manuscript and can be reused for meta-analyses of insecticide responses, population differences in Aedes aegypti, or benchmarking of RNA-seq workflows.

S1 - Counts + Metadata (Supplementary_Data_S1_RNAseq_counts_and_metadata.xlsx):

This file provides sample-level metadata and gene-level count matrices used as input for the differential expression analyses.





Sheet “Sample_metadata” – Sample information for all 18 RNA-seq libraries, including sample ID (e.g. NOC1–NOC3, NOB1–NOB3, NOI1–NOI3, SNC1–SNC3, SNB1–SNB3, SNI1–SNI3), population (New Orleans, San Nicolás), treatment (Control, Broflanilide, Imidacloprid), condition code, and biological replicate.




Sheet “Raw_counts” – Raw gene-level counts produced by featureCounts (rows: NCBI GeneIDs; columns: the 18 libraries). These counts correspond to reads/fragments uniquely assigned to each gene.




Sheet “Filtered_counts” – Subset of the count matrix containing only genes retained for downstream analyses after filtering out lowly expressed genes (total count ≤ 10 across all samples). This matrix was used to build the DESeq2 object and to generate all downstream results



 

S2 - Full DESeq2 results (Supplementary_Data_S2_DESeq2_results_all_comparisons.xlsx):

This file contains complete DESeq2 results for all pairwise comparisons performed in the study.





Sheets “NOB_vs_CNO_all_genes”, “NOI_vs_CNO_all_genes”, “SNB_vs_CSN_all_genes”, “SNI_vs_CSN_all_genes”, “SNB_vs_NOB_all_genes”, “SNI_vs_NOI_all_genes”, “CSN_vs_CNO_all_genes” – For each contrast, all tested genes are reported with standard DESeq2 statistics: baseMean, log₂ fold change, standard error (lfcSE), Wald statistic, raw p-value and Benjamini–Hochberg adjusted p-value (padj), together with the NCBI GeneID.




Sheet “DEG_summary” – Summary table reporting, for each contrast, the total number of genes tested, the number of DEGs with padj < 0.05, and the number of significantly up- and down-regulated genes at padj < 0.05 and |log₂ fold change| > 1.



This file allows users to re-filter DEGs with alternative thresholds and to perform custom downstream analyses.

 

S3 - DEG lists + GO enrichment (Supplementary_Data_S3_DEG_lists_and_GO_enrichment.xlsx)

This file includes filtered lists of significantly differentially expressed genes and the corresponding Gene Ontology enrichment results.





Sheets named “DEGs_<contrast>_sig” (e.g. DEGs_NOB_vs_CNO_sig, DEGs_NOI_vs_CNO_sig, DEGs_SNB_vs_CSN_sig, etc.) – For each contrast, only DEGs with padj < 0.05 and |log₂ fold change| > 1 are reported. Columns include NCBI GeneID, log₂ fold change, padj and an additional “direction” column indicating whether each gene is up- or down-regulated.




Sheets named “GO_BP_<contrast>”, “GO_CC_<contrast>”, “GO_MF_<contrast>” – Gene Ontology Biological Process (BP), Cellular Component (CC) and Molecular Function (MF) enrichment results for each contrast. For every enriched term, the tables include GO term ID, term description, gene and background ratios, p-value, adjusted p-value (padj), q-value, the list of contributing genes, and gene count.



 

To formally test population-specific transcriptional responses to insecticide exposure, we additionally fitted a DESeq2 model including an explicit interaction term between population and insecticide (design = ~ population + insecticide + population:insecticide). This analysis complements the pairwise contrasts reported in the main manuscript by providing a statistical test of whether the effect of each insecticide differs between the New Orleans and San Nicolás populations.

S4 – Population × insecticide interaction: Imidacloprid (Supplementary_Data_S4_DESeq2_interaction_Imidacloprid.csv)

This file contains the full DESeq2 results for the population × imidacloprid interaction term. Each row corresponds to one gene (NCBI GeneID) tested for differential imidacloprid response between populations. Reported columns include baseMean, log₂ fold change for the interaction term, standard error, Wald statistic, raw p-value and Benjamini–Hochberg adjusted p-value (padj). Genes with padj < 0.05 represent loci whose transcriptional response to imidacloprid differs significantly between the New Orleans and San Nicolás populations.

S5 – Population × insecticide interaction: Broflanilide (Supplementary_Data_S5_DESeq2_interaction_Broflanilide.csv)

This file contains the full DESeq2 results for the population × broflanilide interaction term, reported in the same format as Supplementary Data S4. Genes with padj < 0.05 indicate statistically supported population-specific differences in the transcriptional response to broflanilide.