Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus [TC28_FAP_DRUGseq]

ABSTRACT: To investigate the role of FAP in chondrocytes, we transfected an overexpression vector containing cDNA for FAP (Sino Biological; HG10464-UT) into TC28a2 cells using Lipofectamine 3000. We then performed DRUG-seq analysis to determine the impact of FAP on global gene expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE220068 | GEO | 2023/04/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus [TC28_ZEB1_DRUGseq]

Project description:To investigate the role of ZEB1 in chondrocytes, we transfected an overexpression vector containing cDNA for ZEB1 (Sino Biological; HG17705-UT) into TC28a2 cells using Lipofectamine 3000. We then performed DRUG-seq analysis to determine the impact of ZEB1 on global gene expression.

2023-04-19 | GSE220069 | GEO

A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-04-18 | GSE220244 | GEO

A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus [Cartilage_Meniscus_scRNAseq]

Project description:Osteoarthritis (OA) affects all tissues in the knee joint but therapeutic targets have often been selected for their role in cartilage damage and inflammation and largely omitted consideration of mechanisms that are mediating meniscus damage and more importantly there have been insufficient efforts to determine whether pathogenic processes are shared between tissues. Several scRNA-seq analyses have been performed in OA knees but have been largely restricted to the analysis of a single joint tissue of articular cartilage, or meniscus with the exception of one study that analyzed cartilage and synovium. Here, we performed scRNA-seq analyses of healthy and OA-affected human knee cartilage and menisci to interrogate separate and shared mechanisms in cellular homeostasis and OA pathogenesis.

2023-04-19 | GSE220243 | GEO

Krüppel-like factors-4 and -2 are important regulators of joint tissue cells and protect against tissue destruction and inflammation in osteoarthritis [ChIP-seq]

Project description:ChIP-seq with anti-HA tag antibody in TC28a2 cells transfected with HA-KLF4.We performed genome-wide analysis for KLF4-DNA association in TC28a2 human chondrocyte cells, to elucidate regulatory mechanisms of chondrogenic genes by KLF4.

2022-09-11 | GSE183955 | GEO

RNA-Sequencing of EndoC-BH1 cells Overexpressing OAS1, OAS2, or OAS3

Project description:EndoC-BH1 cells were plated in normal media and forward transfected with lipofectamine 3000 (2ug cDNA) of empty, OAS1, OAS2, or OAS3 plasmids from Vector builder

2024-01-01 | GSE244273 | GEO

Krüppel-like factors-4 and -2 are important regulators of joint tissue cells and protect against tissue destruction and inflammation in osteoarthritis [DRUG-seq]

Project description:We performed global gene expression analysis in Ad-KLF4-, Ad-EGFP- and non-transduced TC28a2 human chondrocyte cells, to study genes regulated by KLF4 comprehensively.

2022-09-11 | GSE183954 | GEO

Proteomic Analysis of the Meniscus Cartilage in Osteoarthritis.

Project description:The distribution of differential extracellular matrix (ECM) in the lateral and medial menisci can contribute to knee instability, and changes in the meniscus tissue can lead to joint disease. Thus, deep proteomic identification of the lateral and medial meniscus cartilage is expected to provide important information for treatment and diagnosis of various knee joint diseases. We investigated the proteomic profiles of 12 lateral/medial meniscus pairs obtained from excess tissue of osteoarthritis patients who underwent knee arthroscopy surgery using mass spectrometry-based techniques and measured 75 ECM protein levels in the lesions using a multiple reaction monitoring (MRM) assay we developed. A total of 906 meniscus proteins with a 1% false discovery rate (FDR) was identified through a tandem mass tag (TMT) analysis showing that the lateral and medial menisci had similar protein expression profiles. A total of 131 ECM-related proteins was included in meniscus tissues such as collagen, fibronectin, and laminin. Our data showed that 14 ECM protein levels were differentially expressed in lateral and medial lesions (p < 0.05). We present the proteomic characterization of meniscal tissue with mass spectrometry-based comparative proteomic analysis and developed an MRM-based assay of ECM proteins correlated with tissue regeneration. The mass spectrometry dataset has been deposited to the MassIVE repository with the dataset identifier MSV000087753.

| S-EPMC8348647 | biostudies-literature

Apelin Alleviates Meniscus Endothelial Cell Apoptosis in Osteoarthritis.

Project description:Osteoarthritis (OA) is a degenerative disease characterized by articular cartilage and/or chondrocyte destruction, and although it has long been considered as a primary disease, the importance of meniscus endothelial cell modulation in the subchondral microenvironment has recently drawn attention. Previous studies have shown that apelin could potentially inhibit cellular apoptosis; however, it remains unclear whether apelin could play a protective role in protecting the endothelium in the OA meniscus. In this study, with the advantages of single-cell RNA sequencing (scRNA-seq) data, in combination with flow cytometry, we identified two endothelial subclusters in the meniscus, featured by high expression of Homeobox A13 (HOXA13) and Ras Protein-Specific Guanine Nucleotide Releasing Factor 2 (RASGRF2), respectively. Compared with control patients, both subclusters decreased in absolute cell numbers and exhibited downregulated APJ endogenous ligand (APLN, coding for apelin) and upregulated apelin receptor (APLNR, coding apelin receptor). Furthermore, we confirmed that in OA, decreased endothelial cell numbers, including both subclusters, were related to intrinsic apoptosis factors: one more relevant to caspase 3 (CASP3) and the other to BH3-Interacting Domain Death agonist (BID). In vitro culturing of meniscal endothelial cells purified from patients proved that apelin could significantly inhibit apoptosis by downregulating these two factors in endothelial cell subclusters, suggesting that apelin could potentially serve as a therapeutic target for patients with OA.

| S-EPMC8777459 | biostudies-literature

Loss of function of MALAT1 on primary human OA osteoblast transcriptome

Project description:Cells: Primary human osteoblasts from subchondral bone of osteoarthritis patients (n=3 patients). Treatments: Cells transfected using Lipofectamine 3000 (Qiagen) with either control LNA (NC) or MALAT1 LNA1 or MALAT1 LNA2 for 24 hours. Total RNA extracted by Qiagen RNeasy columns. RIN values >7 via Agilent Bioanalyser. Analysis: RNA subjected to Quantseq 3' RNA sequencing (Lexogen) and sequenced reads mapped to the hg38 reference human genome.

2021-04-28 | GSE167918 | GEO

Effect of BRCA1 overexpression on genetic expressions of cervical cancer based on next generation sequencing

Project description:The cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (Sangon, China) and 1% antibiotic-antimitotic solution (Gibco, USA). The SiHa cells were transfected using Lipofectamine 3000 reagent following the manufacturer’s protocol and incubated for 48h for further analysis.The gene expression profiles were analyzed of SiHa cells transfected with GV230-BRCA1 or GV230 plasmid to assess effect of BRCA1 overexpression on genetic expressions of cervical cancer.

2019-12-06 | GSE141558 | 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