Experimental setup | Methods | Training material (bioinformatics)

Note: If the links below do not work, you can find all the methods in the Google Drive.


Experimental setup

Please find the overview of the experimental workflow here. Alternate link.

Please find the strain selection and bacterial contextual data here.

Please find the sample metadata for the project here. Alternate link.


1) Culture conditions (genome sequencing)

Bacterial pellets for PacBio and MiSeq sequencing were prepared separately from bacterial pellets for RNA, protein and metabolite analyses.


2) Culture conditions (transcript, metabolite and protein analyses)

Bacterial cultures and pellets for RNA, protein and metabolite analyses were prepared in batches for each species. Each culture was split for RNA, metabolite and protein analyses.


3) Workflow for preparing bacterial cultures for omics analyses (RNA, metabolite, protein)

Protocol for bacterial prep
Bacterial prep Escherichia coli.
Bacterial prep Klebsiella pneumoniae
Bacterial prep Staphylococcus aurues
Bacterial prep Streptococcus pneumoniae
Bacterial prep Streptococcus pyogenes

Alternate links here.


4) Omics extractions, data generation workflows and data analyses

4.1) Genomics

gDNA extraction method PacBio RSII and Miseq workflow
gDNA Escherichia coli


PacBio & Miseq Workflow

gDNA Klebsiella pneumoniae
gDNA Staphylococcus aurues
gDNA Streptococcus pneumoniae
gDNA Streptococcus pyogenes

Alternate links here.


4.2) Transcriptomics

RNA extraction method RNAseq workflow
RNA Escherichia coli


RNASeq workflow

RNA Klebsiella pneumoniae
RNA Staphylococcus aureus

RNA Streptococcus pneumoniae

RNA Streptococcus pyogenes

Alternate links here.


4.3) Metabolomics

Metabolomics workflow

Alternate links here.


4.4) Proteomics 

4.4.1) Sample prep

Proteomics sample prep
Proteomics Escherichia coli
Proteomics Klebsiella pneumoniae
Proteomics Staphylococcus aurues
Proteomics Streptococcus pneumoniae
Proteomics Streptococcus pyogenes

Alternate links here.


4.4.2) Protein quantification and spectral library generation

Proteomics workflow

Alternate links here.


5) Training material (bioinformatics)

Training material/tutorials developed by the Research Data Services (RDS) Omics project to analyse omics data can be found here.