Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mass spectrometry data of single-layer and spheroid culture DESC culture medium

ABSTRACT: This dataset originates from a comparative proteomics study of mouse dental epithelial stem cell culture supernatants. The objective of the study was to identify and quantitatively analyse differentially expressed proteins between two experimental groups (labelled Esc2D/EscML and Esc3D/EscSPH in the study) using liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology.

ORGANISM(S): Mus Musculus

SUBMITTER: Lei Lei

PROVIDER: PXD067534 | iProX | Thu Aug 21 00:00:00 GMT+01:00 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Duration of dry and humidified incubation of single-step embryo culture medium and oxygen tension during sham culture do not alter medium composition.

Project description:BackgroundThe extended embryo culture using single-step medium gained popularity in clinical in vitro fertilisation (IVF). However, there are concerns about the degradation of unstable medium components and their negative effects on the developing embryos. Further, dry-incubation can increase osmolality, which can in-turn enhance the concentration of constituents of the media and their stability. Hence, this study was conducted to understand the immediate changes in the culture media constituents in relation to clinically comparable situations such as single-step extended embryo culture and use of dry and humidified-incubation in two-different gaseous conditions.MethodsCommercially available single-step medium was sham-cultured in droplets under oil in two different conditions viz. dry (37°C; 6%CO 2; 5%O 2) and humidified (37°C; 6% CO 2; atmospheric O 2) for 0h, 72h, and 120h intervals. Droplets were subjected to the sensitivity-enhanced nuclear magnetic resonance (NMR)-based profiling using 800 MHz NMR equipped with a cryogenically cooled micro-coil (1.7mm) probe. NMR profile of the embryo culture medium between the two groups were comprehensively assessed.ResultsA total of ten amino acids and four energy substrates were identified from the culture medium. The medium constituents identified showed a non-significant increase in the dry-incubation group at 72h and then declined at 120h. Humidified incubation had no effects on the level of the identified medium constituents until 120h. No significant differences in the levels of medium constituents identified were observed between the dry and humidified-groups at various time-points tested.ConclusionsA non-significant variation in the levels of medium constituents observed in the dry-incubation of single-step medium most unlikely to influence a clinical outcome. However, the impact of these subtle changes on the (epi)genetic integrity of the embryos in a clinical set-up to be addressed.

| S-EPMC9214662 | biostudies-literature

Dental pulp cell-derived powerful inducer of TNF-alpha comprises PKR containing stress granule rich microvesicles (pDCvsGF)

Project description:It is well known that dental pulp tissue can evoke some of the most severe acute inflammation observed in the human body. We found that dental pulp cells secrete a factor that induces tumor necrosis factor-α production from macrophages, and designated this factor, dental pulp cell-derived tumor necrosis factor-α-inducing factor (DPTIF). DPTIF was induced in dental pulp cells and transported to recipient cells via microvesicles. Treatment of dental pulp cells with a PKR inhibitor markedly suppressed DPTIF activity, and weak interferon signals were constitutively activated inside the cells. In recipient macrophages, stimulation with DPTIF-containing supernatants from pulp cells resulted in activation of both nuclear factor-κB and MAP kinases like JNK and p38. Proteomics analyses revealed that many stress granule-related proteins were present in supernatants from dental pulp cells as well as microvesicle marker proteins like GAPDH, β-actin, HSPA8, HSPB1, HSPE1, and HSPD1. Furthermore, giant molecule AHNAK and PKR were detected in microvesicles derived from dental pulp cells, and gene silencing of AHNAK in pulp cells led to reduced DPTIF activity. Thus, it appeared that the core protein of DPTIF was PKR, and that PKR was maintained in an active state in stress granule aggregates with AHNAK and transported via microvesicles. The activity of DPTIF for TNF-α induction was far superior to that of gram-negative bacterial endotoxin. Therefore, we, report for the first time, that active PKR is transported via microvesicles as stress granule aggregates and induces powerful inflammatory signals in macrophages.

2018-12-30 | GSE124491 | GEO

Dental pulp cell-derived powerful inducer of TNF-alpha comprises PKR containing stress granule rich microvesicles (GFvsDP-1)

2018-12-30 | GSE124490 | GEO

Characterization of human dental pulp cells grown in chemically defined serum-free medium

Project description:Dental pulp cells obtained from several donors proliferated actively in a serum-free medium STK2. The growth rate of dental pulp cells from most donors was higher in the serum-free medium than that in a medium containing 10% serum. DNA microarray analyses showed that gene expression profile of dental pulp cells grown in the serum-free medium was similar to that of cells grown in a medium containing 10% serum. However, several genes related to cell proliferation were up-regulated in dental pulp cells grown in the serum-free medium.

2018-03-14 | GSE97199 | GEO

Effects of glucose on gene expression of human dental pulp cells under odontogenic differentiation

Project description:Human dental pulp cells have the ability to differentiate into odontoblast cells under various stimuli. The objective of our study is to investigate the efffects of glucose on gene expression of human dental pulp cells that under go odontogenic differentiation. Expression microarray were performed to identify the genes that were affected by short-term and long-term exposure to high glucose levels.

2022-03-31 | GSE112144 | GEO

Insulin-like Growth Factor Binding Protein 7 identified in aged dental pulp by single-cell RNA sequencing

Project description:Dental pulp plays a crucial role for dental health, and dental pulp aging influences their regenerative and reparative function. However, the underlying molecular mechanisms of dental pulp aging are not exhaustively understood, and thereby an in-depth and complete understanding of the aged dental pulp is of foremost importance. This study aimed to explore the heterogeneity of young and aged dental pulp tissue using single-cell RNA sequencing (scRNA-seq).

2024-12-15 | GSE274562 | GEO

Effect of rosiglitazone treatment on insulin sensitivity in adipose tissue of type 2 diabetic patients

Project description:The goal of this study was to analyse the effect of a 12 weeks treatment with rosiglitazone on insulin sensitivity in the adipose tissue of type 2 diabetic patients. Diabetic patients were submitted to a 3 hours hyperinsulinemic- euglycemic clamp. Adipose tissue biopsies were taken before and after the clamp, labelled A & B respectively. Then, the patients were treated with rosiglitazone, agonist of PPAR gamma, during 12 weeks. After the treatment, all the patients were submitted to a second 3 hours hyperinsulinemic-euglycemic clamp. Adipose tissue biopsies were taken before and after the clamp, labelled C & D respectively.

2018-04-20 | GSE12894 | GEO

Deciphering Black Extrinsic Tooth Stains composition in Children using metaproteomics

Project description:The present study focuses on the use of a metaproteomic approach to analyse Black Extrinsic Tooth Stains, a specific type of pigmented extrinsic substance, in a cohort of 96 Children. Metaproteomics is a powerful emerging technology that successfully enabled human protein and bacterial identification of this specific dental biofilm using mass spectrometry. 1600 bacterial proteins were identified in black stains (BS) samples and 2058 proteins in dental plaque (DP) samples whereas 607 and 582 human proteins identified in (BS and DP, respectively). 132 genera bacteria in black stains and dental plaque were identified using phylopeptidomic analysis, showing prevalence of Rothia, Kingella, Nesseria and Pseudopropionibatcterium in black stains samples. We additionally confirmed the metaproteomic approach by performing 16S rRNA. In this work, we showed an interesting diversity of the microbiota and proteome including significant difference between Black stain and dental plaque samples.

2024-07-25 | PXD029245 | Pride

Arabidopsis seedling hydroponic treatment with Streptomyces AGN23 culture supernatants

Project description:Arabidopsis seedling hydroponic treatment with Streptomyces AGN23 culture supernatants

| PRJNA490893 | ENA

Gene expression in human keratinocytes cultivated with serum-free medium and serum containing medium

Project description:The objective of this study was thus to develop ab initio that chemically defined serum-free medium. We used a statistical design of experiment (DOE) approach to screen a large number of candidate factors, for both their potential individual and synergetic effects, as to identify a formulation which was then tested extensively. In this study, we present the properties of keratinocyte cultivated with serum-Free medium (Surge SFM) and complemented DME-Ham medium (with serum).

2021-09-08 | GSE183594 | 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