Experimental setup | Methods | Training material (bioinformatics)

Experimental setup

Please find the overview of the experimental workflow here.

 

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

 

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

 

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

 

4.3) Metabolomics

Metabolomics workflow

 

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

 

4.4.2) Protein quantification and spectral library generation

Proteomics workflow

 

5) Training material (bioinformatics)

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