Experimental setup | Methods | Training material (bioinformatics)
Consortium Publication & Data Access
The data from this initiative has been published and is publicly accessible from Nature Communications.
https://www.nature.com/articles/s41467-023-37200-w
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)
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 |
|
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 |
|
RNA Klebsiella pneumoniae | |
RNA Staphylococcus aureus | |
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.