https://github.com/sysbiochalmers/proteomereallocationforfastgrowth

Collection of data and scripts for analyzing the proteome allocation of yeast grown in rich and minimal medium
https://github.com/sysbiochalmers/proteomereallocationforfastgrowth

Last synced: 12 months ago
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Collection of data and scripts for analyzing the proteome allocation of yeast grown in rich and minimal medium

• Host: GitHub
• URL: https://github.com/sysbiochalmers/proteomereallocationforfastgrowth
• Owner: SysBioChalmers
• License: mit
• Created: 2020-05-20T15:26:22.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2020-08-19T16:51:02.000Z (almost 6 years ago)
• Last Synced: 2025-01-30T22:51:18.405Z (over 1 year ago)
• Language: R
• Homepage:
• Size: 2.15 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# ProteomeReallocationForFastGrowth

This repository contains a collection of supplementary data and scripts for analyzing and visualizing the data pertaining to the study:

_Proteome re-allocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media._

In this study, _Saccharomyces cerevisiae_ strain CEN.PK113-7D was cultivated in bioreactors with glucose as carbon source with or without supplementation of amino acids, both aerobically and anaerobically.

The main script **Organize_filter_and_quantify_proteomics.R** is used to normalize the TMT data into mass-percentages. The result of running this script is 6 data files named glu_proteomics_\*.csv that are used throughout the analysis. Input data for the script are **TMT_aerobic_cultures.csv**, **TMT_anaerobic_cultures.csv** and **ref2824_iBAQ_unique_peptides.csv**. For the iBAQ-file, fmol/ug amounts and Uniprot accessions were obtained from the proteomics analysis and matched to gene names obtained from Uniprot. All original proteomics data can be obtained from the [PRIDE database](https://www.ebi.ac.uk/pride/) using accession numbers PXD018361 and PXD012803.

  ### Required software

  - R studio (version 1.0.136 or later)