Ontology highlight
ABSTRACT:
PROVIDER: PRJNA771095 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16322560_1.fastq.gz | Fastqsanger.gz | |||
| SRR16322560_2.fastq.gz | Fastqsanger.gz | |||
| SRR16322561_1.fastq.gz | Fastqsanger.gz | |||
| SRR16322561_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Purpose: The goal of this study is to compare (RNA-seq) transcriptomes of in vitro cultured human bone marrow-derived mesenchymal stem cells (hMSCs) and fallow deer antler-derived skeletal progenitors (FD RM Cells) under multiple conditions to identify candidate proliferation and mineralization genes responsible for fast antler regeneration Methods: hMSCs and FD RM Cells were cultured in vitro under 1) serum-free (0% serum) or serum (10% serum) conditions for 2.5 days or 2) Control (0 ng/mL BMP-2 and 0 nM dexamethasone) and osteogenic (100 ng/mL BMP-2 and 100 nM dexamethasone) media for 24 days. mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads were analyzed at the transcript isoform level STARS followed by Cufflinks. Validation for genes of interest was performed using immunofluorescence staining. Results: Comparison of human and fallow deer skeletal progenitor datasets yielded proliferation and mineralization gene candidates Conclusions: Our study represents the first detailed analysis of human and fallow deer transcriptomes of skeletal progenitor cells under proliferation and mineralization conditions, with biologic replicates, generated by RNA-seq technology. Our in vitro comparative approach circumvent some of the logistical and technical challenges in identifying candidate proliferation and mineralization genes responsible for rapid deer antler regeneration. We conclude that in vitro comparison of RNA-seq based transcriptomes identified candidate proliferaiton and mineralization genes to advance bone biology and holds promise to rapidly regenerate large bone volumes for regenerative medicine. The comparative approach utilized here can be adapted for almost any tissue to study a specific phenomenon of interest.
2018-11-16 | GSE89796 | GEO
Project description:We have studied the expression profile of 3D cultured human chondrocytes that were stimulated with supernatant of synovial fibroblasts derived from a RA patient (RASF=HSE cell line) and from a normal donor (NDSF=K4IM cell line), respectively. For this purpose, passage 2 human chondrocytes were cultured for 14 days in alginate beads and subsequently stimulated for 48 hours with supernatant of RASF and NDSF. Baseline expression was determined of unstimulated chondrocytes. Differential genome-wide microarray analysis of RASF and NDSF stimulated chondrocytes disclosed a distinct expression profile related to cartilage destruction involving marker genes of inflammation (COX-2), NF-kappa B signaling pathway (TLR2), cytokines/chemokines and receptors (CXCL1-3, CCL20, CXCL8, CXCR4, IL-6, IL-1beta), matrix degradation (MMP-10, MMP-12) and suppressed matrix synthesis (COMP). Thus, transcriptome profiling of RASF and NDSF stimulated chondrocytes revealed a disturbed catabolic-anabolic homeostasis of chondrocyte function. This study provides a comprehensive insight into the molecular regulatory processes induced in human chondrocytes during RA-related cartilage destruction. Experiment Overall Design: To reveal the RA-related chondrocyte gene expression profile, genome-wide microarray analysis of RASF stimulated human chondrocytes compared to NDSF stimulation was performed. Unstimulated chondrocytes were analyzed for baseline gene expression. For microarray analysis of RASF and NDSF stimulated and unstimulated chondrocytes, respectively, two RNA pools were analyzed, each pool consisting of equal amounts of RNA from three different donors.
2008-06-11 | E-GEOD-10024 | biostudies-arrayexpress
Project description:Bovine articular chondrocytes were grown in micromass culture and were either untreated or treated with 5 ng TGF-b1/ml for 8 hours to identify genes regulated by TGF-b. Six total samples were analyzed. Three biological replicates of untreated bovine articular chondrocytes grown in micromass culture and three biological replicates of bovine articular chondrocytes grown in micromass culture and treated with 5ng TGF-b1/ ml for 8 hours.
2011-09-30 | E-GEOD-29233 | biostudies-arrayexpress
Project description:The process of chondrogenesis in deer antlers is very similar to that of mammalian cartilage formation. Antlers can regenerate at an alarming rate (up to 2 cm per day). To meet the rapid growth of antlers, paracrine factors play an important role. These paracrine factors promote the proliferation and growth of chondrocytes, regulate cartilage development and modulate cartilage phenotype. The application of stem cell paracrine factors for the treatment of cartilage defects avoids the problems of immunocompatibility, tumorigenicity, embolization, and infection. This study demonstrates that ASC-CM can effectively repair cartilage defects using in vitro and in vivo methods, providing a suitable cell source and pathway for cartilage repair and providing ideas for mechanisms to promote cartilage regeneration.
2023-04-11 | PXD041259 | Pride
Project description:Fuchs endothelial corneal dystrophy FECD is a progressive corneal disease that impacts the structure and stiffness of the Descemets membrane DM, a protein layer that serves as a matrix for the corneal endothelial cells CECs. These structural alterations of the DM contribute to the loss of the CECs resulting in corneal edema and blindness. Oxidative stress and TGF-b pathways have been implicated in endothelial cell loss and endothelial to mesenchymal transition of CECs in FECD. Ascorbic acid AA is found at high concentrations in FECD and its impacts on CECs survival has been investigated. However, TGF-b and AA effects on the composition and rigidity of the CECs matrix remain unknown. In this study, we investigated the effect of AA, TGF-b1 and TGF-b3 on the deposition, ultrastructure, stiffness, and composition of the extracellular matrix ECM secreted by primary bovine corneal endothelial cells BCECs. Immunofluorescence and electron microscopy post-decellularization demonstrated a robust deposition and distinct structure of ECM in response to treatments. AFM measurements showed that the modulus of the matrix in BCECs treated with TGF-b1 and TGF-b3 was significantly lower than the controls. There was no difference in the stiffness of the matrix between the AA-treated cell and controls. Gene Ontology analysis of the proteomics results revealed that AA modulates the oxidative stress pathway in the matrix while TGF-b induces the expression of matrix proteins collagen IV, laminin and lysyl oxidase homolog 1. Molecular pathways identified in this study demonstrate the differential role of soluble factors in pathogenesis of the FECD.
| MSV000088172 | MassIVE
Project description:mRNA profiles of primary mouse chondrocytes transfected with control siRNA or Sephs1 siRNA were generated by mRNA sequencing. This study provides insights into the role of SEPHS1 in chondrocytes.
2021-12-01 | GSE179535 | GEO
Project description:mRNA profiles of primary mouse chondrocytes treated with bleomycin, followed by DMSO or ST045849 were generated by mRNA sequencing. This study provides insights into the role of O-GlcNAcylation in chondrocytes.
2024-11-11 | GSE275524 | GEO
Project description:mRNA profiles of primary mouse chondrocytes transfected with miR-Ctrl or miR-204 mimics were generated by mRNA sequencing. This study provides insights into the role of miR-204 in chondrocytes.
2019-02-22 | GSE126846 | GEO