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ProteomicsProteomic stable isotope probing (proteomic SIP) using 13C‑E. coli spike‑ins analyzed by DDA LC–MS/MS
This project applies proteomic stable isotope probing (proteomic SIP) to evaluate detection and quantification of 13C‑labeled E. coli peptides within a complex mouse fecal microbiome background. Proteins were extracted, digested, and quantified before preparing spike‑in mixtures. Mouse fecal peptide...
ORGANISM(S): gut metagenome 
2026-08-30 | PXD075589 | Pride
Proteomic sip  stable isotope probing  metaproteomics  13c labeling  e. coli spike‑in  mouse fecal microbiome  dda  orbitrap fusion 
ProteomicsQuantitative metaproteomic analysis of 13C E. coli spike-in mixtures across dynamic range using Orbitrap Astral DIA LC-MS/MS
This dataset contains label-free DIA LC-MS/MS measurements of controlled bacterial spike-in samples designed to evaluate quantitative performance across a wide dynamic range. The samples consist of defined mixtures of 13C-labeled E. coli peptides spiked into unlabeled backgrounds at different ratios...
ORGANISM(S): gut metagenome 
2026-08-31 | PXD078868 | Pride
13c labeling Dynamic range Dia Stable isotope probing Label-free proteomics Benchmarking Orbitrap astral E. coli spike-in Metaproteomics 
TranscriptomicsOverlapping and unique responses of E. coli to adverse conditions
In the present study we have determined the global gene expression and biomolecular composition in an Escherichia coli model strain exposed to ten adverse conditions (sodium chloride, ethanol, glycerol, two acids (hydrochloric acid and acetic acid), sodium hydroxide, heat (46°C) and cold (15°C) as...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2010-05-18 | E-GEOD-11041 | biostudies-arrayexpress
TranscriptomicsEffect of acetate during Escherichia coli switch from N-Acetyl Glucosamine to Malate
This experiment was performed to challenge E. coli response to acetate when switched from N-Acetyl Glucosamine (NAG) to malate as the main substrate. Here, E. coli BW25113 strain was grown in M9 medium complemented with 15 mM NAG, The cells were grown to mid-exponential phase in shake flasks at 37...
ORGANISM(S): Escherichia coli K-12 
2026-05-12 | E-MTAB-16650 | biostudies-arrayexpress
TranscriptomicsResponse of Escherichia coli to acetate in presence of 100 mM methyl α-D-glucopyranoside
This experiment was performed to challenge E. coli response to acetate when its growth rate flux is reduced by 40% with 100 mM methyl α-D-glucopyranoside. Control without inhibition in the exact same conditions was already published on ArrayExpress database (accession number E-MTAB-9086) and could ...
ORGANISM(S): Escherichia coli K-12 
2022-09-23 | E-MTAB-11717 | biostudies-arrayexpress
TranscriptomicsResponse of Escherichia coli to acetate concentration during growth on glucose
E. coli MG1655 was grown on M9 minimal medium supplemented with 15mM glucose and either 0, 10, 50 or 100 mM acetate. Transcriptomic analysis from exponential growing cells was performed using Agilent microarray A-MEXP-2232. This work was done with the help of students during practicals. Consequentl...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2020-08-21 | E-MTAB-9086 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of wild type E. coli MG1655 versus those with a deletion in the hns gene (Histone-like protein H-NS)
The aim of the experiment was to determine differences in RNA levels between wild-type E. coli and E. coli with an hns deletion. We used RNA-seq, but to control for variation in sample preparation and sequencing, we combined each E. coli RNA sample with a spike-in Salmonella RNA sample of known conc...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2016-06-14 | E-MTAB-4751 | biostudies-arrayexpress
TranscriptomicsDNA methylation analysis of porcine mammary epithelial cells challenged with Escherichia coli
Epigenetic changes such as DNA methylations regulate gene expression patterns in response to environmental cues including infections. Microbial infections induced DNA methylation may play a potential role in modulating host-immune response. In the present study, we sought to determine DNA methylatio...
ORGANISM(S): Sus scrofa 
2019-07-17 | E-MTAB-7363 | biostudies-arrayexpress
TranscriptomicsC. elegans young adults: Exposed to Serratia marcescens versus exposed to E. coli OP50 : 4 hours
Transcriptional profiling of C. elegans young adult worms exposed to pathogen Serratia marcescens for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of patho...
ORGANISM(S): Caenorhabditis elegans 
2012-03-21 | E-GEOD-36499 | biostudies-arrayexpress
TranscriptomicsC. elegans young adults: Exposed to Xenorhabdus nematophila versus exposed to E. coli OP50 : 4 hours
Transcriptional profiling of C. elegans young adult worms exposed to pathogen Xenorhabdus nematophila for 4 hours versus age-matched worms exposed to control lab food E. coli OP50. The goal was to identify genes regulated in response to pathogen. The broader goal of study was to study evolution of p...
ORGANISM(S): Caenorhabditis elegans 
2012-03-21 | E-GEOD-36501 | biostudies-arrayexpress
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