MenW GWAS Phase Variation Data

This repository contains the phase variation data for a set of 163 Neisseria meningitidis MenW:cc11 isolates that were subject to analysis of variation for 11 phenotypic traits from 6 assays (biofilm formation, growth in BHI media, growth in RPMI media, adhesion to A549 eukaryotic cells, release of lactate dehydrogenase activity and a modified serum bactericidal assay). The phase variation data contained in the manuscript associated with this data includes both the repeat numbers and expression states for 11 genes - porA, fetA, nadA, hmbR, hpuA, nalP, mspA, pilC1, pilC2, modA and modB. For the first nine of these genes, this data was obtained from a previous publication. Nevertheless, the repeat numbers of these genes were validate by GeneScan analysis of the isolates stored on the two sets of starter plates used as the inoculums for the phenotypic assays. For the modA and modB genes, de novo data was generated by GeneScan analyses from these DNA extracts. This repository contains the raw gene files and analyses of this raw data.

GeneScan assays were performed using mixing of two to three genes or in some cases individual genes. GeneScan assays involve PCR amplification of the repeat tracts with fluorescently tagged primers and electrophoresis of these products on an auto sequencer. The outputs files (.ab1 or .abi) from the auotsequencer were analysed using PeakScanner on the ThermoFisher website. The files in this repository include the auto sequencer files and Excel files showing how PCR products sizes were converted into repeat numbers and expression states. Data were compared to previously published genomic analyses of these repeat tracts. In some cases PCR products were sequenced by Sanger sequencing to determine the repeat number. This genomic and sequence data was utilised in assigning repeats to fragments of specific sizes. Some alignments of relevant repeat tracts are also included in this database.

Alignments Folder. This folder contains seven sub-folders that contain the alignment data for a specific PV gene. Separate alignments for carriage and disease isolates are provided. Alignments may include sequences upstream and downstream of the repeat tract (required due to contiguous breaks within the repeat tract) and of sequences spanning the repeat tract. All data was generated by performing BLAST searches within the Neisseria PubMLST database where all the genome sequences are available.

MenW-I+II-GeneScan-data Folder. This folder contains three sub-folders - Carriage, Disease and ModA-ModB. The sub-folders contain a folder with a series of Excel files that document the analyses of the PV genes for the plate sets I and II. A separate folder contains auto sequencer output files (.ab1 or .abi) for each of the GeneScan runs.

Sequence-Data folder. This folder contains dideoxysequence files for some of the repeat tracts.