Differential expression of snoRNAs during ATDC5 chondrogenic differentiation
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB45345 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5983520.fastq.gz | Fastqsanger.gz | |||
| ERR5983512.fastq.gz | Fastqsanger.gz | |||
| ERR5983513.fastq.gz | Fastqsanger.gz | |||
| ERR5983514.fastq.gz | Fastqsanger.gz | |||
| ERR5983515.fastq.gz | Fastqsanger.gz |
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Project description:Previously we have shown that the snoRNA RMRP is differentially expressed during chondrogenic differentiation and interference with its function led to important changes in the outcome of chondrogenic differentiation with consequences for ribosomal RNA levels and human disease. To identify additional snoRNAs that may play a role in chondrogenic differentiation, we performed small RNA sequencing (<200 nt) in ATDC5 chondrogenic differentiation at day 0, 7 and 14.
2022-05-01 | E-MTAB-10529 | biostudies-arrayexpress
Project description:Mutations in the RMRP gene are the origin of cartilage-hair hypoplasia. Cartilage-hair hypoplasia is associated with severe dwarfism caused by impaired skeletal development. However, it is not clear why mutations in the RMRP gene lead to skeletal dysplasia. Viperin is a known substrate of RMRP. Since chondrogenic differentiation of the growth plate is required for development of the long bones, we hypothesized that viperin functions as a chondrogenic regulator downstream of RMRP. Viperin protein is expressed throughout the stages of chondrogenic differentiation in vivo. Viperin gene expression is increased during knockdown of Rmrp RNA in the ATDC5 model for chondrogenic differentiation. Viperin is expressed during ATDC5 chondrogenic differentiation. Viperin knockdown reduces, while viperin overexpression increases overall protein secretion, with CXCL10 identified as a potential target via mass spectrometry-proteomics. CXCL10 protein expression is reduced during knockdown and increased during overexpression of viperin and CXCL10 protein expression coincides with viperin expression in ATDC5 chondrogenic differentiation. Viperin knockdown induces, while viperin overexpression reduces TGFβ activity. Furthermore, viperin knockdown conditioned media increases, while viperin overexpression conditioned media reduces chondrogenic differentiation of ATDC5 cells. TGFβ target genes Pai1 and Smad7 are increased during knockdown and reduced during overexpression of viperin. Moreover, TGFβ activity is reduced when differentiating ATDC5 cells are exposed to CXCL10 and, acting as a viperin overexpression mimic, CXCL10 similarly reduces chondrogenic differentiation of ATDC5. Lastly, we show that in CHH patient cells, RMRP expression is reduced and viperin expression is increased, coinciding with reduced chondrogenic differentiation and increased CXCL10 expression, possibly explaining the CHH phenotype. Together our data show that viperin may play a pivotal role in chondrogenic differentiation, with potential consequences for cartilage-hair hypoplasia pathobiology.
2019-02-15 | PXD006999 | Pride
Project description:Chondrogenic differentiation is a coordinated biological process regulated by various cell signalings at both transcriptional and post-transcriptional levels. In this study, microarray was performed to detect the expression profiles of lncRNAs and mRNAs during chondrogenic differentiation of murine chondrogenic cell line ATDC5.
2018-12-28 | GSE124424 | GEO
Project description:Introduction: In addition to the well-known cartilage extracellular matrix-related expression of Sox9, we demonstrated that chondrogenic differentiation of progenitor cells is driven by a sharply defined bi-phasic expression of Sox9: an immediate early and a late (extracellular matrix associated) phase expression. In this study we aimed to determine what biological processes are driven by Sox9 during this early phase of chondrogenic differentiation. Materials: Sox9 expression in ATDC5 cells was knocked-down by siRNA transfection at the day before chondrogenic differentiation or at day 6 of differentiation. Samples were harvested at 2 hours, and 7 days of differentiation. The transcriptomes (RNA-seq approach) and proteomes (Label-free proteomics approach) were compared using pathway and network analyses. Total protein translational capacity was evaluated with the SuNSET assay, active ribosomes with polysome profiling and ribosome modus with bicistronic reporter assays. Results: Early Sox9 knockdown severely inhibited chondrogenic differentiation weeks later. Sox9 expression during the immediate early phase of ATDC5 chondrogenic differentiation regulated the expression of ribosome biogenesis factors and ribosomal protein subunits. This was accompanied by decreased translational capacity following Sox9 knockdown, and this correlated to lower amounts of active mono- and polysomes. Moreover, cap- versus IRES-mediated translation was altered by Sox9 knockdown. Sox9 overexpression was able to induce reciprocal effects to the Sox9 knockdown. Conclusion: Here we identified an essential new function for Sox9 during early chondrogenic differentiation. A role for Sox9 in regulation of ribosome amount, activity and/or composition may be crucial in preparation for the demanding proliferative phase and subsequent cartilage extracellular matrix-production of chondroprogenitors in the growth plate in vivo.
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Project description:To investigate the protective effect of Fascin1 inhibitor NP-G2-044 against chondrocyte dedifferentiation, we stimulated murine chondrogenic cell line ATDC5 cells with IL-1β to induce dedifferentiation, and with or without NP-G2-044 treatment. Gene expression profiling analysis was performed using data obtained from RNA-seq of three independent experiments.
2023-05-27 | GSE232611 | GEO
Project description:mRNAs and lncRNAs expression data of chondrogenic differentiated and undifferentiated murine chondrogenic cell line ATDC5 cells
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Project description:Introduction: In addition to the well-known cartilage extracellular matrix-related expression of Sox9, we demonstrated that chondrogenic differentiation of progenitor cells is driven by a sharply defined bi-phasic expression of Sox9: an immediate early and a late (extracellular matrix associated) phase expression. In this study we aimed to determine what biological processes are driven by Sox9 during this early phase of chondrogenic differentiation. Materials: Sox9 expression in ATDC5 cells was knocked-down by siRNA transfection at the day before chondrogenic differentiation or at day 6 of differentiation. Samples were harvested at 2 hours, and 7 days of differentiation. The mRNA sequencing library was generated using TruSeq mRNA sample preparation kit (Illumina, Eindhoven, the Netherlands). In short, mRNA was enriched using magnetic beads coated with poly-dT, followed by fragmentation. The fragmented mRNA enriched samples were subjected to cDNA synthesis by reverse transcriptase, followed by dA-tailing and ligation of specific double-stranded bar-coded adapters. Next, the library was amplified and following cleanup the sizes of the libraries were determined on an Agilent 2100 Bioanalyzer via a DNA 1000 chip according manufacturer’s protocol. Pooled libraries consisting of equal molar samples were sequenced on a high-output 75bp single read on the NextSeq500 (Illumina). For each sample, the number of reads covering one or more exons of a given transcript were extracted. Triplicates of samples that were treated with either Scrambled or Sox9 siRNAs, at two different time points, were grouped separately. A transcript was defined as expressed when all replicates of a group had at least 5 reads extracted within the transcript's region. The grouped data were then compared to one another. The fold-change difference and the p-value were calculated using R-package edgeR, after which the p-value was corrected for multiple testing (false discovery rate (FDR)-corrected). The transcriptomes using a RNA-seq approach was analyzed using pathway and network analyses. Results: Early Sox9 knockdown severely inhibited chondrogenic differentiation weeks later. Sox9 expression during the immediate early phase of ATDC5 chondrogenic differentiation regulated the expression of ribosome biogenesis factors and ribosomal protein subunits. This was accompanied by decreased translational capacity following Sox9 knockdown, and this correlated to lower amounts of active mono- and polysomes. Moreover, cap- versus IRES-mediated translation was altered by Sox9 knockdown. Sox9 overexpression was able to induce reciprocal effects to the Sox9 knockdown.
2021-06-01 | E-MTAB-10333 | biostudies-arrayexpress
Project description:A comprehensive evaluation of differential gene expression on RNA-seq data of early and late passage hMSCs from three individuals, and undifferentiated and 21-day of chondrogenic differentiation hMSCs from previous publication (GSE109503). Genome-wide RNA-seq and differential expression analysis revealed that signalings such as Pulmonary Fibrosis Idiopathic (IPF) Signaling Pathway and Osteoclasts in Rheumatoid Arthritis (RA) Signaling Pathway were significant differences in early MSC. Differential FOXO1 expression, higher in Early than Late MSCs, was responsible for promoting suspension survival, and cell migration, and induces chondrogenic differentiation.
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Project description:To clarify the important signaling pathways, SE-lncRNAs, and mRNAs associated with SE-lncRNAs regulating chondrogenic differentiation of BMSCs, we assessed the expression of SE-lncRNAs and mRNAs in three pairs of non-induced and the corresponding induced chondrogenic differentiation human Bone marrow-derived mesenchymal stem cells samples by using Human Super-Enhancer LncRNA Microarray. A total of 77 SE-lncRNAs were identified with 47 SE-lncRNAs upregulated and 30 SE-lncRNAs downregaulated as chondrogenic differentiation. 308 mRNAs were identified with 245 mRNAs upregulated and 63 mRNAs downregulated. Some pathways, such as the focal adhesion, extracellular matrix (ECM)-receptor interaction, TGF-b signaling pathway, and PI3K-Akt signaling pathway, were identified as the key pathways may be involved in the chondrogenic differentiation of BMSCs. Moreover, 5 potentially core regulatory mRNAs (PMEPA1, ENC1, TES, CDK6, ADIRF) and 37 SE-lncRNAs in chondrogenic differentiation were revealed by bioinformatic analysis.
2021-10-06 | GSE171106 | GEO