Proteomics

Dataset Information

0

Labeling of Bacillus subtilis and Escherichia coli to saturation with different percentages of fully 13C labeled glucose for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)


ABSTRACT: This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of fully labeled 13C glucose (13C6). Cultures of B. subtilis and E. coli were grown in Bacillus minimal medium or M9 minimal medium (E. coli) in which a percentage of the glucose was replaced with 13C6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C6 glucose were added 0, 0.01, 0.025, 0.1, 0.25, 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Escherichia Coli Bacillus Subtilis Subsp. Subtilis

SUBMITTER: Manuel Kleiner  

LAB HEAD: Manuel Kleiner

PROVIDER: PXD023693 | Pride | 2022-12-30

REPOSITORIES: Pride

Dataset's files

Source:
altmetric image

Publications

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes.

Kleiner Manuel M   Kouris Angela A   Violette Marlene M   D'Angelo Grace G   Liu Yihua Y   Korenek Abigail A   Tolić Nikola N   Sachsenberg Timo T   McCalder Janine J   Lipton Mary S MS   Strous Marc M  

Microbiome 20230209 1


<h4>Background</h4>Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of  ...[more]

Similar Datasets

2022-12-30 | PXD024285 | Pride
2022-12-30 | PXD024287 | Pride
2022-12-30 | PXD024174 | Pride
2022-02-16 | PXD024288 | Pride
2010-02-10 | GSE19014 | GEO
| PRJNA834837 | ENA
2010-02-09 | E-GEOD-19014 | biostudies-arrayexpress
2022-01-21 | PXD028578 | Pride
2013-02-13 | E-GEOD-42223 | biostudies-arrayexpress
2013-02-13 | GSE42223 | GEO