This repository supports Symbiotic T6SS affects horizontal transmission of Paraburkholderia bonniea among Dictyostelium discoideum amoeba hosts. RNA-sequencing data (raw and processed) are available from NCBI GEO GSE276651.
It contains two directories:
phenotype, which contains
- tssh_pheno_analysis.R - R code used to run statistical analyses using the data files and generate figures
- tssH.pheno_fitness.tsv - Data from host fitness experiment with columns in the following order
- date of experiment
- host identity
- symbiont identity
- MOI (multiplicity of infection) of host-symbiont pairing
- percent of host spores infected by symbiont in sample
- percent of spores produced by sample relative to mean of uninfected controls
- symbiont treatment (wildtype or mutant)
- tssH.pheno_transmission.tsv - Data from symbiont transmission experiment with columns in the following
order
- date of experiment
- host identity
- symbiont identity
- MOI of host-symbiont pairing
- percent of host spores infected by symbiont in sample
- percent of infected spores that were previously uninfected
- symbiont treatment (wildtype or mutant)
- tssH.pheno_rescue.tsv - Data from mutant rescue experiment with columns in the following order
- date of experiment
- host identity
- symbiont identity
- MOI of host-symbiont pairing
- percent of host spores infected by symbiont in sample
- percent of infected spores that were previously uninfected
- symbiont treatment (wildtype, mutant, rescue)
RNA-seq, which contains
- alignment_to_count_summary.txt - Summary of pipeline to generate count tables from raw illumina reads
- tssh_de_analysis.R - R code used to run statistical analyses using count files and generate figures
- gene_association.dictybase.filter.gostats.txt - Processed GO annotation file for D. discoideum genome
- endo_phago_path.tsv - Table of D. discoideum genes with known roles in endocytosis and phagocytosis,
with columns in the following order
- gene symbol
- dictyBase gene id
- decription of protein coded by gene
- tssH.de_*.txt - Three DESeq2 summary tables for the time series contrasts performed in the study
- tssH.GO_*.txt - Six GOstats summary tables for the time series contrasts performed in the study; tables for up- and down-regulated groups of genes are separated
- tssH.phago_*.txt - Five tables of phagocytosis-related genes clustered by DEGreport based on expression
change over time in the study, with columns in the following order
- normalized transcript abundance
- timepoint (negative, 090 minutes-post-infection, 360 minutes-post-infection, and positive approximately 2250 minutes-post-infection)
- gene symbol