Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stressosome-independent but RsbT-dependent environmental stress sensing in Bacillus subtilis

ABSTRACT: Proteomic comparison of wild-type B. subtilis PY79, a strain deleted for all stressosome components (rsbRA, rsbRB, rsbRC, rsbRD, ytvA, rsbP, and rsbS) using a clean deletion spanning the rsbRA and rsbS coding sequences, and a strain deleted for all stressosome components but using early stop codons to block translation of RsbRA and RsbS. This comparison was undertaken to learn whether the clean deletion of rsbRA and rsbS has a different impact on the abundance of the proteins that are encoded downstream of these genes. It was also used to corroborate transcriptional reporter data.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Bacillus Subtilis Py79

SUBMITTER: Matthew Cabeen

LAB HEAD: Matthew Thomas Cabeen

PROVIDER: PXD059924 | Pride | 2025-01-20

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1970_1432_0hr_tr1.raw	Raw
	1970_1432_0hr_tr2.raw	Raw
	1970_1432_0hr_tr3.raw	Raw
	1970_1432_60hr_tr1.raw	Raw
	1970_1432_60hr_tr2.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

Quantitative proteomic analysis of co-cultured breast cancer cells

Project description:Aerobic glycolysis is a hallmark of cancer glucose metabolism. Here we suggest that extracellular vesicles (EVs) originating from cancer cells can modulate glucose metabolism in the recipient cancer cells and induce cell proliferation and aggressive cancer phenotypes. Two breast cancer cell lines with different levels of glycolytic activity, MDA-MB-231 and MCF7, were selected and co-cultured, as the originating and recipient cells. The change in 18F-fluorodeoxyglucose (FDG) uptake of the recipient MCF7 cells was assessed after co-culture with the MDA-MB-231 cells. Proteomics analysis was performed to investigate the changes in the protein expression patterns in the recipient MCF7 cells. FDG uptake by the recipient MCF7 cells was sig-nificantly increased after co-culture with the MDA-MB-231 cells.

2022-02-16 | PXD028806 | Pride

Proteomic analysis of human follicular fluid in poor ovarian responders during in vitro fertilization

Project description:Poor ovarian response (POR) observed in controlled ovarian stimulation (COS) is often observed during in vitro fertilization and embryo transfer (IVF-ET) cycles and is a major problem. A POR has been found to be related to several factors, including advanced age, high body mass index, and history of ovarian or pelvic surgery. However, it is difficult to predict POR, as there are no specific biomarkers known. In this study, we used quantitative proteomic analyses to investigate potential biomarkers that can predict poor response during IVF based on follicular fluid samples. A total of 1,079 proteins were identified using a high-resolution orbitrap mass spectrometer coupled online to a nano flow liquid chromatography system. It is notable that 65 up-regulated and 66 down-regulated proteins were found to be functionally enriched in poor responders. We also validated these differentially expressed proteins (DEPs) using a triple-quadrupole (QQQ) mass spectrometer for quantification of targeted proteins. Of the DEPs, three proteins (pregnancy zone protein, renin, and sushi repeat-containing protein SRPX) were regarded as statistically significant (p < 0.05). These proteins (one known as an inhibitor of cell growth and another as a regulator of angiogenesis) are potential biomarkers candidates of POR in IVF.

2018-07-05 | PXD005436 | Pride

Proteomic profiling of cerebrospinal fluid for development of biomarker in medulloblastoma

Project description:Cerebrospinal fluid (CSF) plays an important role in brain tumours, including medulloblastoma (MBL). CSF proteomics studies have mainly focused on extracellular vesicle (EV) proteins rather than the total CSF proteome. Recent advancements in mass spectrometry systems and �쁎mics�� data analysis methods enable unbiased, high proteome depth research. We conducted proteomic profiling of the total CSF in MBL patients with the purpose of finding a potential diagnostic biomarker for MBL. Methods CSF samples from patients with MBL (n=31) and hydrocephalus (HC, control, n=19) were analysed using liquid chromatography-tandem mass spectrometry (LC�묺S/MS). Enrichment analysis of canonical pathways and differentially expressed proteins (DEPs) was performed. Feature selection of the proteins was conducted using the analysis of variance F value and fast correlation-based filter methods. The selected proteins were validated through ELISA and EV characterization using ExoView systems. Results We quantified 1,112 proteins per CSF sample. We further investigated 273 DEPs extracted from a comparison of MBL and HC. Hierarchical clustering of DEPs between MBL and HC clearly showed classification into two groups. Feature selection identified four elevated soluble proteins (SPTBN1, HSP90AA1, TKT, and NME1-NME2) in MBL CSF. Validation with ELISA confirmed that TKT was significantly elevated in MBL compared to HC, as well as in Group 4 MBL and leptomeningeal seeding (LMS). Additionally, TKT-positive EVs were significantly enriched in MBL CSF compared to HC CSF and correlated with the burden of LMS. Conclusions Our results provide insights into the proteomics data of the total CSF of MBL patients. Furthermore, we identified the significance of TKT within the total CSF and its presence within circulating EVs in the CSF. We suggest that TKT may serve as a biomarker for MBL, particularly for the diagnosis of LMS.

2024-08-29 | PXD045982 | Pride

Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma

Project description:Alterations in chromatin accessibility independent of DNA methylation can affect cancer-related gene expression, but are often overlooked in conventional epigenomic profiling approaches. In this study, we describe a cost-effective and computationally simple assay called AcceSssIble to simultaneously interrogate DNA methylation and chromatin accessibility alterations in primary human clear cell renal cell carcinomas (ccRCC). Our study revealed significant perturbations to the ccRCC epigenome, and identified gene expression changes that were specifically attributed to the chromatin accessibility status whether or not DNA methylation was involved. Compared to commonly mutated genes in ccRCC, such as the von Hippel-Lindau (VHL) tumor suppressor, the genes identified by AcceSssIble comprised distinct pathways and more frequently underwent epigenetic changes, suggesting that genetic and epigenetic alterations could be independent events in ccRCC. Specifically, we found unique DNA methylation-independent promoter accessibility alterations in pathways mimicking VHL deficiency. Overall, this study provides a novel approach for identifying new epigenetic-based therapeutic targets, previously undetectable by DNA methylation studies alone, that may complement current genetic-based treatment strategies. Examination of 3 different histone modifications in 2 patient tumor and adjacent normal samples.

2016-03-15 | E-GEOD-75597 | biostudies-arrayexpress

Interactome analysis of Adenylyl cyclase-associated protein 1

Project description:The direct inflammatory action of proprotein convertase subtilisin/kexin type 9 (PCSK9) is examined in vitro in monocytes and endothelial cells, as well as via an in vivo atherosclerosis animal model. PCSK9 exacerbates atherosclerosis in low-density lipoprotein receptor (LDLR)-/- mice, indicating an inflammatory effect mediated independently of the LDLR pathway. Here we show that Adenylyl cyclase-associated protein 1 (CAP1) is the main binding partner of PCSK9, serving a crucial role in the pro-inflammatory cascade of PCSK9 by enabling the induction of cytokines, the activation of Toll-like receptor 4 (TLR4), and the upregulation of scavenger receptors. We also present spleen tyrosine kinase (Syk) and protein kinase C delta (PKCδ) as pivotal mediators in the inflammatory cascade subsequent to PCSK9-CAP1 binding. In human peripheral blood mononuclear cells (PBMCs), serum PCSK9 levels are positively correlated with Syk, PKCδ, and p65 phosphorylation. Notably, the CAP1-fragment crystallizable region (CAP1-Fc) shows superior efficacy in mitigating PCSK9-mediated inflammatory signal transduction when compared with the PCSK9 inhibitor, evolocumab.

2024-06-16 | PXD047058 | Pride

Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human brain

Project description:5-hydroxymethylcytosine (5-hmC) is a newly discovered modified form of cytosine that has been suspected to be an important epigenetic modification in neurodevelopment. While DNA methylation dynamics have already been implicated during neurodevelopment, little is known about hydroxymethylation in this process. Here we report DNA hydroxymethylation dynamics during cerebellum development in the human brain. Overall, we find a positive correlation between 5-hmC levels and cerebellum development. Genome-wide profiling reveals that 5-hmC is highly enriched on specific gene regions, including exons and especially the untranslated regions (UTRs), but it is depleted on introns and intergenic regions. Furthermore, we have identified fetus-specific and adult-specific differentially hydroxymethylated regions (DhMRs), most of which overlap with genes and CpG island shores. Surprisingly, during development DhMRs are highly enriched in genes encoding mRNAs that can be regulated by fragile X mental retardation protein (FMRP), some of which are disrupted in autism, as well as in many known autism genes. Our results suggest that 5-hmC-mediated epigenetic regulation may broadly impact the development of the human brain, and its dysregulation could contribute to the molecular pathogenesis of neurodevelopmental disorders. We generated comprehensive genome-wide profiles of 5hmC in human cerebellum.

2012-09-30 | E-GEOD-40539 | biostudies-arrayexpress

Single-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity

Project description:We report a single-cell whole-genome bisulfite sequencing method (scBS-Seq) capable of accurately measuring DNA methylation at up to 36% of CpGs. We observed that ESCs grown in serum/LIF or 2i/LIF both display epigenetic heterogeneity, with M-bM-^@M-^\2i-likeM-bM-^@M-^] cells present in serum cultures. In silico integration of 12 individual MII oocytes datasetsM-BM- recapitulates the whole DNA methylome, making scBS-Seq a versatile tool to explore DNA methylation in rare cells and heterogeneous populations. scBS-Seq has been performed on mouse MII oocytes for technical validation and on mouse ESCs cultured in 2i/LIF and serum/LIF to investage epigenetic heterogeneity

2014-07-18 | E-GEOD-56879 | biostudies-arrayexpress

Dissecting psa locus regulation in Yersinia pestis

Project description:We looked at H-NS bound sites in wild type Yersinia pestis and in a mutant strain in which the psaE gene was deleted.

2021-06-01 | E-MTAB-10694 | biostudies-arrayexpress

Arabidopsis thaliana peptide SP2 and ethyl acetate extraction clean up.

Project description:The success of bottom-up proteomic analysis frequently depends on the efficient removal of contaminants from protein or peptide samples before LC-MS/MS. For a peptide clean-up workflow, the single-pot solid-phase-enhanced peptide sample preparation on carboxylate-modified paramagnetic beads (termed SP2) was evaluated for sodium dodecyl sulfate or polyethylene glycol removal from Arabidopsis thaliana tryptic peptides. The robust and efficient 40-min SP2 protocol, tested for a 10 ng, 250ng and 10µg peptide sample, was proposed and benchmarked thoroughly against the ethyl acetate extraction protocol. The SP2 protocol on carboxylated magnetic beads proved to be the robust approach even for simultaneous removal of massive sodium dodecyl sulfate (SDS) and polyethylene glycol (PEG) contaminations from AT peptide samples in respect of the LC-MS/MS data outperforming ethyl acetate extraction.

2024-01-03 | PXD045031 | Pride

Strome Mes-4, H3K36me3 and H3K27me3 in N2 EEMB

Project description:ChIP-chip of Mes-4, H3K36me3 and H3K27me3 in N2 C. elegans early embryo EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: N2; Sex: population predominantly Hermaphrodites perhaps with some Males; NUMBER OF REPLICATES: 2 or 3; EXPERIMENTAL FACTORS: temperature 20

2012-05-29 | E-GEOD-38180 | biostudies-arrayexpress

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