Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Translation Accuracy in E. coli

ABSTRACT: We present a method that quantifies nearly all pairwise amino acid substitutions, revealing the rates and spectra of mistranslation per amino acid and per codon.

INSTRUMENT(S):

ORGANISM(S): Escherichia Coli

TISSUE(S): Cell Culture

SUBMITTER: Ryan Stikeleather

LAB HEAD: Michael Lynch

PROVIDER: PXD064116 | Pride | 2025-06-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	218-1.mzML	Mzml
	218-1.mzid	Mzid
	218-1.raw	Raw
	218-2.mzML	Mzml
	218-2.mzid	Mzid

Items per page:

1 - 5 of 34

Similar Datasets

Comparative microarray analysis of NaV1.8-expressing DRG neurons and cold-sensitive non-NaV1.8-expressing DRG neurons

Project description:The vast majority of cold sensitive DRG neurons from mice do not express the voltage-gated sodium channel NaV1.8. Therefore, we aimed to compare the molecular profiles of NaV1.8 and non-NaV1.8-expressing neurons using microarray analysis. Fluorescent activated cell sorting was performed at 4 degrees centigrade on acutely dissociated DRG neurons from mice expressing NaV1.8-Cre, Pirt-GCaMP3 and a Cre-dependent global reporter (td tomato). NaV1.8-expressing neurons were sorted based on their reporter fluorescence (td tomato; red) and putative cold sensing neurons were sorted based on their GCaMP3 fluorescence at 4 degrees centigrade and absence of Cre-dependent reporter fluorescence. A total of three mice were used (samples one, two and three) with GCaMP3 only and NaV1.8-expressing neurons forming two relative populations within each sample (eg. GC3 one is the experimental counterpart of Tom one).

2019-07-01 | E-MTAB-7070 | biostudies-arrayexpress

Mass spectrometry-based proteomic exploration of diverse murine macrophage cellular models

Project description:Immortalised cell lines analogous to their primary cell counterparts are fundamental to research, particularly when large cell numbers are required. Here we report that immortalisation of bone marrow-derived macrophages using the J2-virus resulted in the loss of a protein of interest, MSR1, in wild-type cells by an unknown mechanism. This led us to perform an in-depth mass spectrometry-based proteomic characterisation of common murine macrophage cell lines (J774A.1, RAW264.7, and BMA3.1A7), with comparison to the immortalised bone marrow-derived macrophages (iBMDMs), as well as primary BMDMs. This revealed striking differences in protein profiles associated with macrophage polarisation, phagocytosis, pathogen recognition, and IFN signalling. J774A.1 cells were determined to be the most similar to the gold standard primary BMDM model, with BMA3.1A7 cells the least similar due to the reduction in abundance of several proteins related closely to macrophage function. This comprehensive proteomic data offers valuable insights into the selection of specific macrophage cell lines for cell signalling and inflammation research.

2024-10-28 | PXD051067 | Pride

Liver-derived plasminogen mediates muscle stem cell expansion during caloric restriction through the plasminogen receptor, Plg-RKT. Bareja, White, Et. Al.

Project description:Quantitative label free proteomic characterization of liver secretomes in mice fed either ona regular or calorie restricted diet.

2024-06-16 | PXD043644 | Pride

Plasma membrane proteomics of tumors +/- AP2, Zimmerman and Counter

Project description:Area under the curve label free quantitative proteomics on membrane enriched sampels from tumors +/- AP2 complex.

2024-12-13 | PXD042404 | Pride

JEC21 CN phosphoproteomic study, Yadav and Heitman

Project description:Label free quantititative phosphoproteomics analysis following TiO2 enrichment, nanoscale capillary chromatography and high resolution tandem mass spectrometry.

2025-08-21 | PXD059891 | Pride

Microarray of neural progenitor cells from neonatal lung injury mice treated with placebo or umbilical-cord mesenchymal stromal cell extracellular vesicles or untreated, as well as age-matched control mice

Project description:The purpose of this experiment was to determine the transcriptional differences between neural progenitor cells from neonatal lung injury mice vs. control mice, as well as neonatal lung injury mice treated with umbilical-cord mesenchymal stromal cell extracellular vesicles vs. neonatal lung injury mice treated with placebo (PBS). Neural progenitor cells were isolated from the subventricular zone and hippocampus and cultured for 2 consecutive neurosphere assays. RNA was then extracted from the cells, and the microarray labelling, hybridization, and scanning was conducted by the Génome Québec Innovation Centre (Montréal, Canada).

2022-05-17 | E-MTAB-11157 | biostudies-arrayexpress

Microarray data of the subventricular zone and hippocampal tissue from mice exposed to room air or hyperoxia during the neonatal period

Project description:This experiment aimed to investigate the differences in the transcriptional profile of the neurogenic niche regions of mouse pups that were raised in room air verses mouse pups that were exposed to hyperoxia during the neonatal period. Pups were housed in room air or hyperoxia (85% O2) from P0 to P14. Brain tissue (the subventricular zone and the hippocampus) was collected at P14 and 12 months of age. RNA was extracted from the brain tissue and the microarray labelling, hybridization, and scanning was conducted by the Génome Québec Innovation Centre (Montréal, Canada).

2023-01-03 | E-MTAB-11332 | biostudies-arrayexpress

Gene expression profiling of human whole-blood samples before and after the administration of recombinant human erythropoietin

Project description:As part of cross-platform comparisons of microarray and RNA-seq, this current experiment using the Affymetrix Human Transcriptome Array 2.0 aimed to quantify gene-level expression in subjects administered recombinant human erythropoietin over a 10-week protocol for the identification of gene signatures of blood doping. These results were compared to results obtained from other gene expression quantification platforms using the same experimental cohort, including the Illumina HumanHT-12v4 Expression BeadChips (archived in ArrayExpression; E-MTAB-2874), Illumina NextSeq 500 and MGI DNBSEQ-G400RS.

2021-11-04 | E-MTAB-11080 | biostudies-arrayexpress

A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts

Project description:Chemical activators and inhibitors are useful probes to identify substrates and downstream effects ofenzymes; however, due to the complex signaling environment within cells, it is challenging to distinguishbetween direct and indirect effects. This is particularly the case for phosphorylation, where a single(de)phosphorylation event can trigger rapid changes in many other phosphorylation sites. An additionalcomplication arises when a single catalytic entity, which acts in form of many different holoenzymes withdifferent substrates, is activated or inhibited, as it is unclear which holoenzymes are affected, and in turnwhich of their substrates are (de)phosphorylated. Direct target engaging MS-based technologies to studytargets of drugs do not address these challenges. Here, we tackle this by studying the modulation of proteinphosphatase-1 (PP1) activity by PP1-disrupting peptides (PDPs), as well as their selectivity toward PP1, byusing a combination of mass spectrometry-based experiments. By combining cellular treatment with the PDPwith in vitro dephosphorylation by the enzyme, we identify high confidence substrate candidates and beginto separate direct and indirect effects. Together with experiments analyzing which holoenzymes areparticularly susceptible to this treatment, we obtain insights into the effect of the modulator on the complexnetwork of protein (de)phosphorylation. This strategy holds promise for enhancing our understanding of PP1in particular and, due to the broad applicability of the workflow and the MS-based read-out, of chemicalmodulators with complex mode of action in general.

2024-01-12 | PXD044415 | Pride

Poss_Pronobis BioID2 Zebrafish Interaction Proteomics

Project description:BioID2 Zebrafish Interaction Proteomics analyzed by nanoscale capillary LC coupled to a Fusion Lumos OT with label-free quantitation.

2025-08-27 | PXD046501 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data