"Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights on the genetic basis of survival of pathogenic mycobacteria"
Amanda J Gibson1,5&*, Jennifer Stiens2*, Ian J Passmore3, Valwynne Faulkner1,6&, Josephous Miculob1, Sam Willcocks3, Michael Coad4, Stefan Berg4, Dirk Werling1, Brendan W Wren3, Irene Nobeli2, Bernardo Villarreal-Ramos4,5&, Sharon L Kendall1**
1Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, AL9 7TA 2Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX 3London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT 4Animal and Plant Health Agency, Woodham Ln, Addlestone, Surrey, KT15 3NB 5Centre of Excellence for Bovine Tuberculosis, IBERS, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3EE 6Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, 1 Midland Road, London 15 NW1 1AT & current address *the authors contributed equally to the work **corresponding author
The repository includes a markdown document, "Methods_process.Rmd" which outlines the steps taken to analyse the Tn-seq files
The python scripts used in the methods are found in 'scripts' directory.
R code for making the plots in the paper are in 'plot_code', and the lists of genes used are in 'gene_lists' directory.
An dataframe including all the resampling data from all of the cattle samples is included as 'R_data/resamp_data.RData'. Resampling using pooled lung or node samples is contained in dataframes 'R_data/lung_pooled.RData' and 'R_data/node_pooled.RData'
Insertion files in .wig for each sample are found in 'insertion_files' directory.
Data_files includes: prot tables, reference sequences, list of TA sites per gene, and the list of genes with zero insertions
