Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome-wide analysis by LC-MS/MS reveals the role of ATRA during adipogenesis in hBMSCs

ABSTRACT: To investigated the role of all-trans retinoic acid (ATRA) in protein expression profiling during human bone mesenchymal stem cells (hBMSCs) adipogenesis. Liquid chromatography tandem mass spectrometry(LC-MS/MS) was used to determine the protein profile,and raw data were analyzed against the UniProt database using MaxQuant with the Andromeda search engine.

ORGANISM(S): Homo Sapiens

SUBMITTER: Jun Cao

PROVIDER: PXD065247 | iProX | Fri Jun 20 00:00:00 BST 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Glomus sp. MS strain:MS

Project description:Glomus sp. MS strain:MS Genome sequencing

| PRJNA210520 | ENA

Methanosarcina barkeri MS strain:MS

Project description:Methanosarcina barkeri MS strain:MS Raw sequence reads

| PRJNA613292 | ENA

Expression genes induced by intermittent mechanical stress (MS) in human periodontal ligament (PDL) cells

2010-12-20 | GSE26077 | GEO

Extracellular vesicles from osteogenic differentiated human BMSCs

Project description:Pathological processes like osteoporosis or steroid-induced osteonecrosis of the hip are accompanied by increased bone marrow adipogenesis. Such disorder of adipogenic/osteogenic differentiation, which affects also bone marrow derived mesenchymal stem cells (BMSCs) contributes to bone loss during aging. Therefore, we investigated the effects of extracellular vesicles (EVs) isolated from human (h)BMSCs during different stages of osteogenic differentiation on osteogenic and adipogenic differentiation capacity of naïve hBMSCs.

2022-10-14 | PXD035845 | Pride

EC-exosomes and BM fluid-Exosomes

Project description:We isolated the exosomes from mouse bone marrow fluid, mouse primary bone marrow endothelial cells (BMEC) culture supernatants of WT-BMEC and Vps33b knockdown BMECs by ultracentrifugation. After characterization of isolated exosomes, A global comparison of the protein cargo carried by the different exosomes. In brief，protein were extracted and labeled with TMT, the peptide were subjected to NSI source followed by tandem mass spectrometry (MS/MS) in a Q Exactive HF-X (Thermo) coupled with an EASY-nLC 1200 UPLC system, and the resulting MS/MS data were processed using the MaxQuant search engine.

2020-11-24 | PXD020946 | Pride

MANF interactomes by AP-MS method in two mammalian cell lines, the HEK293 and INS1

Project description:AP-MS approach to identify MANF-interacting proteins from HEK293 and INS1 cell lines. Proteins were identified and MS1 quantified using Andromeda search engine and MaxQuant proteomics software 92. Thermo .raw files were searched against the human or rat component of the UniProt-database complemented with trypsin, BSA, GFP and tag sequences

2020-10-21 | MSV000086342 | MassIVE

Super-SILAC analysis of human lung primary tumor-derived xenografts LC-MS/MS

Project description:Non-small cell lung cancer (NSCLC) accounts for 85% of lung cancers, and is subdived into 2 major histological subtypes: adenocacinoma (ADC) and squamous cell carcinoma (SCC). Super-SILAC methodology was used to facilitate the quantitative comparisons of human primary tumor-derived xenograft proteomes by high resolution MS analysis. Xeno092 and Xeno441 were ADCs. Xeno 561 and Xeno691 were SCCs. Principal component analysis and supervised t-tests revealed differentially expressed proteins responsible for the classification of the samples according to their distinctive proteomes. These results confirm known differentiators between ADC and SCC subtypes of NSCLC (e.g. a keratin signature, cell adhesion molecules, and metabolism proteins), and reveal novel candidates that may be useful to classify and treat NSCLC tumors. The raw files were analyzed by MaxQuant (version 1.3.0.5). Peaks were searched against the UniProt human database (released Jul, 2012; http://www.uniprot.org) using the Andromeda search engine included in MaxQuant. Two miscleavages were allowed and at least six amino acids per identified peptide were required. The false discovery rate for peptides and proteins was set at 0.01. 'Match between runs' option was selected within a time window of 2 min. A minimum ratio count of 2 was used for quantification of SILAC pairs. Further data analysis was performed in Perseus.

2014-01-28 | PXD000438 | Pride

Expression genes induced by intermittent mechanical stress (MS) in human periodontal ligament (PDL) cells

Project description:Excessive MS is known to result in disappearance of the alveolar hard line, enlargement of thePDL space, and destruction of alveolar bone, leading to occlusal traumatism. The regulatory role of MS is believed to play a critical role in the process of alveolar bone remodeling. However, little is known about the effect of excessive MS on expression of osteoclastogenesis-related genes in human PDL cells. Human PDL cells were cultured in silicon chambers, which was attached to a stretching apparatus (STB-140; Strex Co. Ltd., Osaka, Japan) The cells were allowed to attach to the chamber base for 48 hours, after which uniaxial sinusoidal stretching (conditions: 60 sec/returns, resting time; 29 sec, stretch length; 1.6 mm, stretch ratio; 105%) was applied at 37°C, 5% CO2. We compared to the genes expression between 0 and 48 hours after MS stimulation.

2010-12-20 | E-GEOD-26077 | biostudies-arrayexpress

Differentially expressed adipocyte-associated genes in Bone-marrow Mesenchymal stem cells under normal and hypoxic conditions

Project description:To identify proteins involved in the regulation of adipogenic differentiation under hypoxic conditions, an RT2 Profiler PCR array was used to screen a panel of 84 genes associated with human adipogenesis in Bone-marrow Mesenchymal stem cells under normal and hypoxic conditions. Bone-marrow Mesenchymal stem cells were put in hypoxic chamber, set at an oxygen concentration of 0.2%. Cells under normoxia are considered as a control.

2015-02-11 | E-GEOD-65842 | biostudies-arrayexpress

Genome-wide analysis of the transcriptional profile of the CNS in MS patients.

Project description:We identify cellular heterogeneity during in MS patient samples from the CNS Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

2020-02-12 | GSE129762 | 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