Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Escherichia coli proteome during outgrowth from stationary phase

ABSTRACT: We studied the proteomic dynamics of Escherichia coli cells exiting stationary phase and identified unique dynamics for the proteins.

INSTRUMENT(S):

ORGANISM(S): Escherichia Coli

TISSUE(S): Cell Culture

SUBMITTER: Handuo Shi

LAB HEAD: Kerwyn Casey Huang

PROVIDER: PXD023729 | Pride | 2021-01-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	LZ03092020_proteins.xlsx	Xlsx
	e034042.raw	Raw
	e034046.raw	Raw
	e034050.raw	Raw
	e034054.raw	Raw

Items per page:

1 - 5 of 16

Similar Datasets

Escherichia coli proteome upon sudden carbon starvation

Project description:We studied the proteome changes in Escherichia coli growing in rich media, and compared the changes between exponential phase cells and those underwent sudden carbon starvations.

2021-03-09 | PXD024151 | Pride

METTL21C methylates Alanine tRNA synthetase at lysine 943 in muscle tissue

Project description:Protein lysine methylation is a common post-translational modification (PTM) detected throughout the human proteome that plays important roles in diverse biological processes. In the human genome, there are greater than one hundred known and candidate protein lysine methyltransferases (PKMTs), many with important links to human disease. METTL21C (methyltransferase-like protein 21C) is a PKMT implicated in muscle biology and reported to methylate VCP (valosin-containing protein/p97) and HSPA8 (heat shock 70kDa protein 8). However, a clear in vitro methyltransferase activity for METTL21C is yet to be demonstrated. Thus, whether METTL21C is indeed an active enzyme that directly methylates substrate/s is unclear. Here, we use an unbiased biochemical-based screening assay coupled to mass spectrometry to identify Alanine-tRNA-Synthetase 1 (AARS1) as a direct substrate of METTL21C. METTL21C catalyzes mono-, di- and tri-methylation of lysine 943 of AARS1 (AARS1-K943me) in vitro and in vivo. In vitro methylation of AARS1 by METTL21C is independent of ATP or tRNA molecules. In contrast to AARS1, and in conflict with previous reports, we do not detect METTL21C methylation activity on VCP and HSPA8. Depletion of METTL21C in METTL21C-expressing cells leads to depletion of AARS1-K943 methylation. Finally, METTL2C is almost exclusively expressed in muscle tissue, and accordingly we detect the METTL21C-catalyzed methylation event of AARS1 in mouse skeletal muscle tissue. Together, our work identifies AARS1 as a bona fide substrate of METTL21C and suggests a role for the METTL21C-AARS1 axis in the regulation of protein synthesis in muscle tissue. In addition, our study describes a straightforward protocol for elucidating physiologic substrates of little characterized or uncharacterized PKMTs

2020-07-02 | PXD019886 | Pride

Phosphoproteomics of Arabidopsis flg22 treated nuclear samples

Project description:To study the effect of microbe-associated molecular pattern (MAMP) treatment (flg22) on the phosphorylation of nuclear proteins, we treated Arabidopsis plants with flg22 and after isolation of nuclear proteins, we enriched for phosphopeptides and then carried out LC-MS/MS analyses. We used statistical analysis tools to identify differentially phosphorylated proteins in response to MAMP treatment in the mock and treated samples.

2022-02-28 | PXD008403 | Pride

Using Shewanella baltica ecotypes as a model for transcriptional variation

Project description:Assessment of individual whole cell transcriptional variation among closely related bacterial ecotypes Here we used 4 replicates each containing 3 independent biological replicates as well as dye swaps per each replicate. We hybridized in a two color format but analyzed in a one color format.

2012-04-30 | E-GEOD-37672 | biostudies-arrayexpress

A peptide CORO1C-47aa encoded by circ-0000437 functions as a negative regulator in endometrium tumor angiogenesis

Project description:Circular RNAs (circRNA) are a novel class of widespread non-coding RNAs (ncRNAs) that regulate gene expression in mammals. Recent studies demonstrate that functional peptides can be encoded by short open reading frames (sORFs) in ncRNAs, including circRNAs. In this study, through deep RNA sequencing on human endometrial cancer (EC) samples and their paired adjacent normal tissues, we uncovered that the circRNA hsa-circ-0000437 is significantly reduced in EC compared to matched paracancerous tissue. The hsa-circ-0000437 contains a sORF encoding a functional peptide termed as CORO1C-47aa. Overexpression of CORO1C-47aa is capable of inhibiting angiogenesis at the initiation stage by suppressing endothelial cell proliferation, migration, and differentiation through competing with TACC3 to bind to ARNT and suppress VEGF. The anti-tumor effects of CORO1C-47aa on EC progression suggest that CORO1C-47aa has a potential value in anti-carcinoma therapies and deserves further investigation.

2022-02-17 | PXD026046 | Pride

Chromatin signatures at Notch regulated enhancers reveal large-scale changes in H3K56ac upon activation

Project description:To investigate the influence of chromatin organization and dynamics on the response to Notch signaling, we partitioned Drosophila chromatin using histone modifications and established This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-07-01 | E-GEOD-66227 | biostudies-arrayexpress

Revealing the Structural Plasticity of SARS-CoV-2 nsp7 and nsp8 Using Structural Proteomics (XL-MS)

Project description:SARS-CoV-2 nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase and other nspsHere we used solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS), illuminate the dynamics of SARS-CoV-2 full-length nsp7, nsp8, and nsp7:nsp8 proteins and protein complex.

2022-01-12 | PXD026191 | Pride

Single-nuclei RNA-sequencing of Arabidopsis thaliana plant tissues Arabidopsis thaliana using a nanowell-based system

Project description:Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nuclei isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as alternative to the use of protoplast isolation, which is currently the standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nuclei isolation method by using different plant materials from different species. The potential of our snRNA-seq method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors underlying this process and predicted potential target genes of these transcription factors. Our nuclei isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.

2021-09-05 | E-MTAB-9174 | biostudies-arrayexpress

Saccharomyces cerevisiae sorted and untreated

Project description:Gene expression of a vital, stained and sorted subpopulation of Saccharomyces cerevisiae with high affinity to glucose, harvested at a dilution rate of D=0.160 h-1, and of cells from the whole population without further treatment grown at the same dilution rate were analysed. The isolation of RNA was accomplished by using lyticase to lyse the cells and the Qiagen RNeasy Mini Kit with some modifications within the manufacturers´ protocol. 6 µg of the total RNA per sample was used for each microarray experiments. The indirect labelling by the tyramide-signal-amplification method (MicromaxTM TSATM labelling and detection Kit from Perkin Elmer life sciences) was used to increase the Cy3 and Cy5 signals of microarray detection. Each cDNA containing Biotin- and Fluorescein-nucleotides respectively was purified with a QIAquick PCR purification kit and suspended in 11 µl of the formamide containing hybridization buffer. The slides were hybridized at 42°C over night under a cover slip. The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software. Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes. Microarray experiments were realised with dye swap and cDNA labelling was proceeded in loop design.

2007-10-01 | E-GEOD-8247 | biostudies-arrayexpress