Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly barcoded transposons (RB-TnSeq)

by K. M. Wetmore, M. N. Price, R. J. Waters, J. S. Lamson, J. He, C. A. Hoover, M. J. Blow, J. Bristow, G. Butland, A. P. Arkin, A. M. Deutschbauer. (2015) mBio, doi: 10.1128/mBio.00306-15

This page includes the raw and processed fitness data, along with code to make figures.

Mini web sites with data tables for each bacterium:

• Escherichia coli K-12 (the parent strain for the Keio deletion collection)
• Shewanella oneidensis MR-1
• Shewanella amazonensis SB2B
• Phaeobacter inhibens BS107
• Pseudomonas stutzeri RCH2

Source code:

• R code for plots -- to be run in this R image (103 MB)
• Scripts for reproducing the mini web sites and other tables read in by the R code (22 MB)
  • instructions
  • analysis steps and log from running them
• FEBA code repository

Larger Downloads:

• The reads (fastq files) (355 GB)
  • Listing of files
  • Mapping to original sequencing names
• The mini web sites and other tables that are read in by the R code (3.5 GB)
• Test data sets:
  • TnSeq data for E. coli only (tarball, 4.9 GB)
  • For a small BarSeq data set, see the MiSeq run for E. coli growing on glucose