https://doi.org/10.5061/dryad.j0zpc86p3

This repository is divided into four main folders (.zip) and contains R scripts (.Rmd format) and raw data files (.txt, .xlsx and .csv format) to reproduce the results from the 58-day survival experiment, the worker survival in the oxidative stress experiment, the fecundity analyses of workers and queens, the head width measurement as well as the gene expression analysis of the worker and queen dataset. We further provide the scripts for gene ontology enrichment analyses and the Blastx outputs for the different lists of DEGs (workers and queens) together with the corresponding DESesq2 output files.

Description of the data and file structure

All R scripts are in .Rmd format and input raw files in either .txt, .xlsx or .csv format.

The folder "survival_analyses.zip" contains script "58_Day_survival_Tapinoma_workers.Rmd" and the corresponding raw data file "58_Day_survival.xlsx" to replicate the results from out 58-day survival experiment. The folder further holds the script "Tapinoma_OxidativeStress_Survival.Rmd" and the corresponding raw data file "oxidative_stress_survival.txt" to run the survival analysis from the oxidative stress experiment. All abbreviations that are explained at the beginning of each R script in the "key" section.

The folder "fecundity_analyses.zip" is divided in two separate folders:

1. queen_fecundity: The script "TapinomaQueens_Ovaries.Rmd" and the corresponding raw data file "Ovaries_Q.xlsx" to analyse queen mean ovariole length and the number of developing oocytes dependent to age. 
2.  worker_ovarian_development:  The script "Ovaries_Tapinoma_workers_Jan23.Rmd" and the corresponding raw data file "Ovaries_TapinomaWorker_Jan23.txt" to analyse differences in ovarian development (mean ovariole length and oocyte number) dependent to queen number and worker location.

The folder "head_width_measurements.zip" contains the script "head_width_TapinomaWorkers.Rmd" to examine head width differences between large and small workers ("head_width_workers.txt")

The folder "gene_expression_analysis.zip" is divided into four distinct folders:

1. worker_gene_expression: This folder holds the script "DESeq2_Tapinoma_workers.Rmd" with the corresponding gene count table "TmagW_htseqcounts.RData" and the meta data file "sample_file_WorkerTapi_RSEM.txt" to analyse gene expression changes based on queen number and worker location
2. queen_gene_expression: This folder holds the script "DESeq2_Tapinoma_queens.Rmd", the corresponding gene count table "Tmag_htseqcounts.RData" and the meta data files "sample_file_QueensTapi_rsem" (with all brain and fat body samples) as well as "sample_file_QueensTapi_rsem_filtered.txt" (excluding one brain sample with a low mapping rate) to analyse age-related gene expression changes in young and old Tapinoma magnum queens. 
3. gene_annotation: This folder contains the Blastx output for the DEGs explained by an interaction between queen number and worker location ("Blast_DESeq2_DEGs_interaction_queen_number_worker_location.xlsx"), and the Blastx output for the DEGs explained by worker location only ("Blast_DESeq2_DEGs_worker_location.xlsx"), as well as the Blastx outputs for the DEGs explained by age in the queens ("Blast_DESeq2_DEGs_Queen_age.xlsx"). All these files also contain the corresponding DESeq2 output files with the lists of DEGs within multiple sheets in the excel file. Moreover, we provide an additional folder ("TopGO_analysis") which holds the script "TopGO_worker_location_Tapinoma.Rmd"and the database "tapinoma_go_term_database_final_combined_unique_gene_out.txt" to replicate the GO enrichment analyses for  the list of DEGs upregulated in inside workers ("upInside.txt") and the DEGs upregulated in outside workers ("upOutside.txt").
4. overlapping_DEGs_queens_workers: This folder contains the scrip "overlappingDEGs_queens_workers.Rmd" that identifies the common gene pool between queens and workers with the files "queen_contigs_55349.csv" and "worker_contigs_73277.csv" to then examine the statistical significance of the overlapping DEGs between workers and queens using Fisher's exact tests. We also provide the file "overlapping_DEGs_workers_vs_queens.xlsx" with the lists of overlapping genes between workers and queens including Blast annotations. 

Each folder contains column explanations for the data files used in the analyses. Additional details can be found in the respective R scripts. 

Sharing/Access information

This data is not publicly accessible elsewhere.