Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Peptidomics analysis of urine from IC/BPS patients and healthy controls

ABSTRACT: Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic and debilitating pain disorder of the bladder and urinary tract with poorly understood etiology. A definitive diagnosis of IC/BPS can be challenging because many symptoms of IC/BPS are shared with other urological disorders. An analysis of urine presents an attractive and non-invasive resource for monitoring and diagnosing IC/BPS. Here, a non-targeted LC-MS and LC-MS/MS-based peptidomics analysis of urine samples collected from IC/BPS patients were compared to urine samples from asymptomatic controls.

INSTRUMENT(S): Xevo G2-XS Tof

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

DISEASE(S): Interstitial Cystitis

SUBMITTER: James Checco

LAB HEAD: James Checco

PROVIDER: PXD031843 | Pride | 2022-06-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20201217patient_urine_S001.raw.rar	Raw
	20201217patient_urine_S002.raw.rar	Raw
	20201217patient_urine_S003.raw.rar	Raw
	20201217patient_urine_S004.raw.rar	Raw
	20201217patient_urine_S005.raw.rar	Raw

Items per page:

1 - 5 of 177

Similar Datasets

Saccharomyces cerevisiae: DSB mapping by Break-chip in a two-color experiment (G1 control vs. S phase samples)

Project description:Break-chip (microarray-based double strand break mapping) analysis of mec1 cells recovering from 200 mM hydroxyurea in the presence or absence of 0.8 micromolar bathophenanthroline sulfonate (BPS). We asked if the presence of an iron chelator, BPS, during cell recovery from transient exposure to 200 mM hydroxyurea changes the global patterns of DNA double strand breaks (DSBs). We used a yeast checkpoint mutant, mec1, which has been shown to produce DSBs at replication forks after hydroxyurea was removed from the cell culture. We synchronously released cells from the G1/S transition into S phase in the presence of 200 mM hydroxyurea. After 1h treatment, the drug was removed and cells were allowed to recover in fresh medium for 1h in the presence or absence of 0.8 micromolar BPS. Recover (R) samples, R-1h-BPS and R-1h+BPS, as well as the G1 control samples were collected. Break-chip analysis was performed as previously described (Feng et al., G3(Bethesda) 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554).

2015-01-12 | E-GEOD-64446 | biostudies-arrayexpress

Oral exposure to bisphenol S is associated with alterations in oviduct proteome with aggravated effects in overweight females in an ovine model

Project description:In mammals, the final maturation and transport of gametes, fertilization and early embryo development take place in the oviducts. Bisphenol S (BPS) is a substitute for bisphenol A in plastic manufacturing and, as a potential endocrine disruptor, may alter the oviduct physiology. Furthermore, bisphenols are fat-soluble and can accumulate in fatty tissues. The objective of this study was to assess the effect of a daily dietary exposure to BPS combined with a contrasted diet on the oviduct fluid (OF) proteome using an ovine model. Eighty adult cyclic ewes were allotted to four groups (20/group): over-fed consuming in their diet 50 µg/kg/day of BPS, under-fed consuming 50 µg/kg/day of BPS, and non-exposed controls in each diet group. After three months, the mean body condition score and plasma levels of glucose and non-esterified fatty acids were significantly higher in over- than in under-fed females. The proteins in collected OF samples (50 µg) were analyzed by nanoliquid chromatography coupled with tandem mass spectrometry (nanoLC-MS/MS). Overall, 1563 proteins were identified, among which 848 were quantified. Principal component analysis of data revealed a clear discrimination of samples according to the diet and a segregation between BPS-exposed and non-exposed females in over-fed ewes. Hierarchical clustering of differentially abundant proteins (DAPs) identified two clusters of 101 and 78 DAPs according to the diet. Pairwise comparisons between groups revealed a stronger effect of BPS in over- than in under-fed females (70 vs. 24 DAPs) and a stronger effect of the diet in BPS-exposed than non-exposed females (56 vs. 36 DAPs). Functional analysis of DAPs showed an enrichment in metabolic processes, immune system, cell response to stress, and reproductive processes. This work highlights for the first time the important impact of BPS on the oviduct proteome with bigger effects in over- than underweight females.

2024-05-28 | PXD044858 | Pride

Different exercise modalities have distinct effects on the transcriptome profile in the male rat femoral diaphysis

Project description:Mechanical loading is a key determinant of bone mass, geometry and strength and is essential to maintain optimal skeletal health. We hypothesized that spontaneous low-impact exercise would affect global gene transcript levels in cortical bone of growing rats. We used RNA-Seq to analyse the transcriptome of the femoral mid-diaphysis in pre-pubertal male rats that were assigned to one of three exercise groups for 15 days: control (CON); bipedal stance (BPS); and wheel exercise (WEX). RNA-seq analysis identified 808 and 324 differentially expressed transcripts in the BPS and WEX animals, respectively. In WEX animals, the up-regulated transcripts were enriched for gene ontology terms associated with bone metabolism. Both BPS and WEX animals showed changes in transcripts that were enriched for muscle-related processes. However, in WEX these transcripts were down-regulated while in BPS such transcripts were up-regulated. Importantly, we observed that the exercise mode had diametrically opposite effects on transcripts for multiple genes within the integrin-linked kinase (ILK) and Ca2+ signalling pathways such that they were up-regulated in BPS and down-regulated in WEX. The findings are important for our understanding of possible ways in which different exercise regimens might affect bone when normal activities apply mechanical stimuli during post-natal growth and development. 24 weanling (21 day old) male Sprague-Dawley rats were assigned to three exercise groups .After the 15 day trial period, total RNA was extracted from the femoral diaphysis and mRNA profiles were analysed using RNA-seq

2015-11-02 | E-GEOD-67787 | biostudies-arrayexpress

Homo sapiens strain:Human | isolate:bladder | breed:Aisan | cultivar:bladder

Project description:IC/BPS bladder genome sequencing

| PRJNA692316 | ENA

Oral exposure to bisphenol S associated with alterations in the proteome of granulosa cells in ewes with contrasted metabolic status.

Project description:Bisphenol S (BPS) is a substitute for bisphenol A in plastic manufacturing, the BPA being an endocrine disruptor that alters granulosa cell (GC) functions. Furthermore, bisphenols are able to modulate lipid metabolism and adipogenesis. The aim of this study was therefore to characterise the effects of chronic exposure to BPS on the proteome of ewe GCs considering the interaction between metabolism and reproductive function. Forty adult cyclic ewes were divided into two groups with contrasted diets: restricted (R, n=20) and well-fed (WF, n=20). Within each group, two subgroups were defined according to BPS exposure (0 and 50 µg/kg/day) to generate 4 final groups: R0 and R50 for the restricted ewes, WF0 and WF50 for the well-fed ewes. After three months, the mean body condition score and plasma levels of glucose and non-esterified fatty acids were significantly higher in well-fed than in restricted females. After synchronization of the ewes, GC samples were collected from preovulatory follicles, few hours before the presumptive ovulation. After washing of the cells, the proteins in collected GCs samples (50 µg) were analyzed by nanoliquid chromatography coupled with tandem mass spectrometry (nanoLC-MS/MS). Overall, 1004 proteins were identified, among which 882 were quantified. Principal component analysis of data revealed that all the conditions are quite distinct from one another, and there is a clear separation between ewes on a restricted diet and those on a well-fed diet. Hierarchical clustering of differentially abundant proteins (DAPs) identified five clusters of DAPs, and three cluster have unique protein profile for one condition. Functional analysis of DAPs showed an enrichment in metabolic processes, immune system and cell response to stress. This study is the first reporting and comparing the entire proteome of granulosa cells from ewes exposed or not to chronic BPS exposure with a contrasted diet.

2024-11-07 | PXD047107 | Pride

Study of gene networks in basal progenitors during cortical neurogenesis

Project description:During cortical development neurons are generated sequentially from basal progenitors (BPs) which specifically express the transcription factor Tbr2. We used fluorescent-activaed cell sorting (FACS) to isolate BPs from Tbr2GFP knockin reporter mice (Arnold SJ et al. Genesis, 2009) at early (embryonic day, E13) and late (embryonic day, E16) stages of cortical neurogenesis and determined mRNA expression profiles using mouse mRNA microarray (Illumina MouseWG-6 v2). Comparison of E13 and E16 mRNA expression profiles allowed us to identify regulatory gene networks for maintaining stage specific homeostasis of BPs throughout neurogenesis. FACS isolated BPs at E13 and E16 mouse brain cortex were used for microarray analyses. Six biological replicates (embryonic cortex from three different litters) for E13 and five biological replicates (embryonic cortex from three different litters) for E16 were analysed.

2014-05-01 | E-GEOD-45450 | biostudies-arrayexpress

Study of miRNAs function in basal progenitors during cortical neurogenesis

Project description:During cortical development neurons are generated sequentially from basal progenitors (BPs) which specifically express the transcription factor Tbr2. We used fluorescent-activaed cell sorting (FACS) to isolate BPs from Tbr2GFP knockin reporter mice (Arnold SJ et al. Genesis, 2009) at early (embryonic day, E13) and late (embryonic day, E16) stages of cortical neurogenesis and determined miRNA expression profiles using mouse miRNA microarray (Agilent).Comparison of E13 and E16 microRNA expression profiles allowed us to identify regulatory mechanisms for maintaining stage specific homeostasis of BPs. FACS isolated BPs at E13 and E16 mouse brain cortex were used for miRNA microarray analyses. Four biological replicates (embryonic cortex from three different litters) for each group (E13 or E16) were analysed.

2014-05-01 | E-GEOD-45449 | biostudies-arrayexpress

Anaerobic biogas plants via LC-MS/MS

Project description:Anaerobic degradation (AD) of heterogeneous agricultural substrates is a complex process involving a diverse microbial community. While microbial community composition of a variety of biogas plants (BPs) is well described, little is known about metabolic processes and microbial interaction patterns. Here, we analyzed 16 large-scale BPs using metaproteomics. All metabolic steps of AD were observed in the metaproteome, and multivariate analyses indicated that they were shaped by temperature, pH, volatile fatty acid content and substrate types. Biogas plants can be subdivided into hydrogenotrophic, acetoclastic or a mixture of both methanogenic pathways based on their process parameters, taxonomic and functional metaproteome. Network analyses showed large differences in metabolic and microbial interaction patterns. Both, number of interactions and interaction partners were highly dependent on the prevalent methanogenic pathway for most species. Nevertheless, we observed a highly conserved metabolism of different abundant Pseudomonas spp. for all BPs indicating a key role during AD in carbohydrate hydrolysis irrespectively of variabilities in substrate input and process parameters. Thus, Pseudomonas spp. are of high importance for robust and versatile AD food webs, which highlight a large variety of downstream metabolic processes for their respective methanogenic pathways.

2019-11-11 | PXD014605 | Pride

Candida Iron deprived Cells: Control vs. BPS treated

Project description:Transcriptional profiling of iron deprived Candida cells comparing the WT vs BPS (Iron deprived) cells One-condition experiment, WT vs. BPS treated cells. Biological replicates: 3 control, 3 treated, independently grown and harvested.

2010-11-17 | E-GEOD-25394 | biostudies-arrayexpress

Single cell RNA-seq of bladder tissue

Project description:We report the application of single cell RNA-seq for transcript profiling in bladder tissue from Interstitial cystitis/bladder pain syndrome (IC/BPS) with Hunner lesions and without Hunner lesions and normal tissue.

2024-05-23 | GSE175526 | GEO

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