Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Overexpression of four and a half LIM domains protein 2 promotes epithelial-mesenchymal transition-like phenotype in fish pre-osteoblasts

ABSTRACT: Four and a half LIM domains protein 2 (FHL2) is a co-regulator of gene transcription relevant for many signalling pathways and physiological processes. In this work, the role of FHL2 in cell differentiation has been investigated during in vitro mineralization using a Sparus aurata pre-osteoblast cell line (VSa16, [1]). A global microarray analysis was then performed to characterize the molecular pathways affected by FHL2 overexpression. [1] Pombinho, A.R., Laizé, V., Molha, D.M., Marques, S.M.P. and Cancela, M.L. (2004). Development of two bone-derived cell lines from the marine teleost Sparus aurata; evidence for extracellular matrix mineralization and cell-type specific expression of matrix Gla protein and osteocalcin. Cell Tissue Res. 315, 393-406.

ORGANISM(S): Sparus aurata

PROVIDER: GSE32501 | GEO | 2013/01/03

SECONDARY ACCESSION(S): PRJNA147777

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Overexpression of four and a half LIM domains protein 2 promotes epithelial-mesenchymal transition-like phenotype in fish pre-osteoblasts

Project description:Four and a half LIM domains protein 2 (FHL2) is a co-regulator of gene transcription relevant for many signalling pathways and physiological processes. In this work, the role of FHL2 in cell differentiation has been investigated during in vitro mineralization using a Sparus aurata pre-osteoblast cell line (VSa16, [1]). A global microarray analysis was then performed to characterize the molecular pathways affected by FHL2 overexpression. [1] Pombinho, A.R., LaizM-CM-), V., Molha, D.M., Marques, S.M.P. and Cancela, M.L. (2004). Development of two bone-derived cell lines from the marine teleost Sparus aurata; evidence for extracellular matrix mineralization and cell-type specific expression of matrix Gla protein and osteocalcin. Cell Tissue Res. 315, 393-406. Sparus aurata oligo-DNA microarray (GPL6467) was used to compare gene expression profiles between Control (WT) and FHL2-transfected (F2) VSa16 cell lines. Gene expression profiles of both WT and F2 cells were assessed either at T0 (initial confluent cultures) or T4 (4 weeks of cell confluency). Four (4) pools of cells were taken from both WT and F2 groups at each time point and stored in RNA later at -20M-BM-0C until RNA extraction.

2013-01-03 | E-GEOD-32501 | biostudies-arrayexpress

Comparison of gene expression profile of gilthead seabream mineralization-induced VSa13 cells against controls

2011-06-01 | GSE18915 | GEO

Comparison of gene expression profile of gilthead seabream mineralization-induced VSa16 cells against controls

2011-06-01 | GSE18941 | GEO

Comparison of gene expression profile of gilthead seabream mineralization-induced VSa13 cells against controls

Project description:In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) was used to compare expression profiles of mineralization-induced VSa13 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change. In this study, we analyzed six (6) cell samples, three (3) collected from untreated VSa13 cell cultures and three (3) collected from mineralization-induced VSa13 cell cultures. Gene expression profiling was performed using Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) (6 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal that was left after all the FE processing steps was ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

2011-06-01 | E-GEOD-18915 | biostudies-arrayexpress

Comparison of gene expression profile of gilthead seabream mineralization-induced VSa16 cells against controls

Project description:In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GEO accession: GPL6467) was used to compare expression profiles of mineralization-induced VSa16 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change. In this study, we analyzed six (6) cell samples, three (3) collected from untreated VSa16 cell cultures and three (3) collected from mineralization-induced VSa16 cell cultures. Gene expression profiling was performed using Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) (6 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal that was left after all the FE processing steps was ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

2011-06-01 | E-GEOD-18941 | biostudies-arrayexpress

Sparus aurata transcriptomic data comparing long-term starvation and feeding with three diets differing in the macronutrient composition

Project description:Agilent custom-made 8x60k 60-mer oligonucleotide microarray slides were used, covering unique sequences (21,093 annotated sequences and 4,299 unannotated sequences) of Sparus aurata transcriptomic data obtained from assembling of reads deposited in the NCBI SRA database corresponding to BioProject ID PRJNA391557, together with controls (8 transcripts of Sparus aurata plus Agilent controls). Two probes per sequence were used (in sense orientation for annotated sequences).

2017-10-31 | GSE100744 | GEO

Transcriptome analysis of gilthead sea bream (Sparus aurata) brain after exposure to environmental concentrations of human pharmaceuticals

Project description:A gilthead sea bream (Sparus aurata) microarray platform was developed to identify brain gene expression profiles in response to environmental concentrations of human pharmaceuticals.

2014-05-22 | GSE38195 | GEO

Identification of vitamin K-dependent proteins in mouse liver by LC-MS/MS

Project description:Vitamin K (VK), a fat-soluble vitamin, functions as a co-factor during the gamma-carboxylation reaction that converts glutamic acid residues to gamma-carboxyglutamic acid residues in proteins transiting through the endoplasmic reticulum. Two enzymes are involved which together form the VK cycle: gamma-glutamyl carboxylase (GGCX), and vitamin K oxidoreductase (VKORC1). GGCX requires reduced VK (VKH2) as an essential cofactor, which upon carboxylation, is oxidized to VK epoxide and then reconverted to VKH2 by VKORC1. Physiologically, gamma-carboxylation is essential in the liver for the activity of several coagulation factors (e.g., prothrombin, factor IX, etc.), and in arteries and cartilage to modulate the activity of Matrix Gla Protein (MGP) which prevents extra-osseous tissue mineralization. Gamma-carboxylation also negatively regulates the function of osteocalcin, a bone-derived hormone that promotes glucose homeostasis. Our objective is to identify unrecognized gamma-carboxylated proteins.

2023-05-10 | PXD032920 | Pride

Function of LIM-only protein FHL2 in vascular smooth muscle cells

2014-10-07 | GSE56860 | GEO

Function of LIM-only protein FHL2 in vascular smooth muscle cells

Project description:The LIM-only protein FHL2 is expressed in SMCs and inhibits SMC-rich lesion formation. However, the underlying mechanism behind FHL2's action in SMCs has been only partially resolved. To further elucidate the role of FHL2 in SMCs we compared the transcriptome of cultured SMCs derived from wild-type (WT) and FHL2-knockout (KO) mice. Comparison of gene expression in aortic smooth muscle cells (SMCs) isolated from WT and FHL2-knockout (FHL2-KO) mice. SMCs isolated from three mouse aortas were pooled (Kurakula et al, PLOS One, 2014). Both for WT and FHL-KO mice three batches of SMCs (derived from 9 mice) were cultured. The SMCs were grown to confluency and maintained in serum-free medium for 48 hrs before harvest. Subsequently, RNA was isolated for gene expression profiling.

2014-10-07 | E-GEOD-56860 | 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