CampAttack PV Data
This data set consists of the raw and analysed GeneScan data for two in vivo experiments with a range of Campylobacter jejuni strains. The in vivo experiments involved inoculation of multiple chickens with C. jejuni strain M1 or strains of lineages ST353 and ST464. Bacteria were recovered from the inoculum, at 14 days post inoculation (experiment 1) or 7 and 14 days post inoculation (experiment 2). Bacteria were recovered from the caecal contents, ileal contents, spleen homogenates or liver homogenates. For splean and liver, bacteria were recoved from direct plating only, after enrichment only or both.
PV expression states were estimated from either colonies or sweeps collected from a low dilution plate. Each folder contains the data for one specific strain (NCTC11168 and M1 or only M1) or combined data for multiple strains of two lineages (ST353 and ST464). The folders also have maps of the 96 well plates into which the DNA extracts from the bacterial colonies and sweeps were arranged.
Each Excel files contains a series of tabs. The Notes tab indicates the contents of the file, source of the data and updates performed on the data. Other tabs encompass the raw data from extracted from analysis of the raw GeneScan files, colony and sweep data for each repeat number of a locus where available, the ON percentage for samples where relevant and in some cases summary data utilised for regression analyses.
The List-of-samples and Maps file contain the information on the treatment groups (strains/pens) and the number of samples collected for each bird and for each isolation site. The files also indicate how samples were arrayed into plates for the GeneScan analysis.
The Raw_GeneScan_Data folders contain a series of sub-folders for the GeneScan analysis of each 96 well plate of DNA samples. Each of these folders contains the following files and sub-folders:- Caro_xxx_plate_yy.txt (output information from ABI autosequencer), genescan_plate_x.xlsx (plate map and input information for autosequencer), plate_x_results.details (.csv, .xlsx, .out.html; contains complete output information from psanalyse); plate.x.results.pjc (project file created by PeakScanner); plate_x_results.score (.csv, .xlsx; these are the expression scores for each gene for each colony); plate_x_results.tracts.csv (repeat number data for each gene of each colony); plate_x_results.scores.txt (expression state data for each gene of each colony); six folders containing the ABI output files for each well of the 96 well plate.
The Exp_2_Comparison_colonies+sweep_inoculum contains a comparison of the percentages for the ON states and repeat numbers of every gene as obtained for sweep versus colony data. The file contains separate tabs for each lineage and a combined data set.
The Six-gene-phasotypes-Expt-1 folder contans four Excel files with the data for six gene phasotypes for each colony of all samples. The phasotype data was generated using a sweep correction algorithm using experimental data from sweep PV and colony PV data (as generated by PCR and GeneScan). These files contain the diversity and divergence scores and the input data for the Network diagrams and Decimal graphs of phasotypes. A word document to describe this data is also included.
