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Gene expression and alternative splicing data from human cartilage endplate-derived stem cells

ABSTRACT: Low back pain (LBP) is one of the most prevalent conditions which need medical advice and result in chronic disabilities. Degenerative disc disease (DDD) is a common reason for LBP. A lot of researchers think that CEP degeneration play critical roles in the initiation and development of DDD. In recent years, researchers have put interests on cell-based therapies for regenerating disc structure and function. Our research team has isolated cartilage endplate-derived stem cells (CESCs) and validated their chondrogenic and osteogenic differentiation ability. Enhanced chondrogenic differentiation and inhibited osteogenic differentiation of CESCs may retard CEP calcification and restore the nutrition supply, possibly regenerating the degenerated discs. We used Affymetrix Human Transcriptome Array 2.0 to study the global gene expression profilling and alternative splicing events during the chondrogenic and osteogenic differentiation of cartilage endplate-derived stem cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE63897 | GEO | 2015/12/21

SECONDARY ACCESSION(S): PRJNA269360

REPOSITORIES: GEO

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Gene expression and alternative splicing data from human cartilage endplate-derived stem cells

Project description:Low back pain (LBP) is one of the most prevalent conditions which need medical advice and result in chronic disabilities. Degenerative disc disease (DDD) is a common reason for LBP. A lot of researchers think that CEP degeneration play critical roles in the initiation and development of DDD. In recent years, researchers have put interests on cell-based therapies for regenerating disc structure and function. Our research team has isolated cartilage endplate-derived stem cells (CESCs) and validated their chondrogenic and osteogenic differentiation ability. Enhanced chondrogenic differentiation and inhibited osteogenic differentiation of CESCs may retard CEP calcification and restore the nutrition supply, possibly regenerating the degenerated discs. We used Affymetrix Human Transcriptome Array 2.0 to study the global gene expression profilling and alternative splicing events during the chondrogenic and osteogenic differentiation of cartilage endplate-derived stem cells. The cartilage endplate-derived stem cells(CESCs) were induced to undergo chondrogenic(CD) and osteogenic differentiation(OD). Both undifferentiated and differentiated CESCs were sent for RNA extraction and hybridization on Affymetrix microarrays. A comparative analysis was done between the undifferentiated and differentiated samples.

2015-12-21 | E-GEOD-63897 | biostudies-arrayexpress

Expression data of osteogenic differentiated cartilage endplate-derived stem cells (CESCs) under hypoxia or normoxia

Project description:Cartilage endplate-derived stem cells (CESCs) with chondro-osteogenic differentiation capacity may be responsible for the balance of chondrification and ossification in cartilage endplate (CEP). CEP is an avascular and hypoxic tissue, and hypoxia could inhibit the osteogenic differentiation of CESCs. We used high-throughput scanning to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) during osteogenic differentiation of CESCs under hypoxia compared to those induced under normoxia. Human cartilage endplate-derived stem cells (CESCs) were treated with osteogenic differentiation medium under normoxia and hypoxia for 21 days respectively.

2016-06-14 | E-GEOD-83284 | biostudies-arrayexpress

Expression data of osteogenic differentiated cartilage endplate-derived stem cells (CESCs) under hypoxia or normoxia

2016-06-14 | GSE83284 | GEO

Expression and alternative splicing data of cartilage endplate-derived stem cells (CESCs) under hypoxia or normoxia

Project description:Cartilage endplate-derived stem cells (CESCs) with chondro-osteogenic differentiation capacity may be responsible for the balance of chondrification and ossification in cartilage endplate (CEP). CEP is an avascular and hypoxic tissue, and hypoxia could influence the fate of CESCs. We used high-throughput scanning to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) of CESCs under hypoxia compared to those under normoxia. Human cartilage endplate-derived stem cells (CESCs) were cultured under normoxia and hypoxia for 21 days respectively.

2016-07-18 | E-GEOD-84484 | biostudies-arrayexpress

Expression and alternative splicing data of cartilage endplate-derived stem cells (CESCs) under hypoxia or normoxia

2016-07-18 | GSE84484 | GEO

Proteomic Signature of Nucleus Pulposus of Human Intervertebral Disc

Project description:Intervertebral Disc (IVD) degeneration leading to Low back pain (LBP) is the most common musculoskeletal disorder. Lack of knowledge on the intricate homeostatic mechanisms necessitates proteomic characterisation of a normal human IVD to understand the biological process and unravel the pathomechanisms of degenerative disc disease (DDD). In this study, we employed proteomic approach coupled with tandem mass-spectrometry to derive the comprehensive list of proteins expressed in true biologically normal control discs. This would serve as the basis for identifying the interacting molecules participating in significant biological processes and pathways disrupted during aging and degeneration.

2021-09-09 | PXD016560 | Pride

Single-cell RNA-seq in a comparative primate skeletal cell culture model [1]

Project description:We evaluated the degree to which gene expression patterns in primate skeletal cells differ across cell types and species. First, we optimized differentiation protocols of human and chimpanzee iPSCs through an intermediate MSC state and into chondrogenic or osteogenic cells. Single-cell RNA sequencing was collected from each stage of differentiation (iPSCs, MSCs, chondrogenic cells, and osteogenic cells) using the 10X Genomics platform to characterize gene expression variation.

2022-02-10 | GSE167240 | GEO

Different expression profiles of lncRNAs, mRNAs and circRNAs in degenerative and healthy cervical cartilage endplate (ceRNA)

Project description:The degeneration of cartilage endplate in cervical disc is considered as a basis of cervical spondylosis. Owing to the important role of post-transcriptional gene regulation in phenotypes and functions of cells, non-coding ribonucleic acid (ncRNA) molecules contributed to the regulation.Degenerated cervical vertebral endplate cartilage specimens were collected from patients with cervical intervertebral disc degeneration (CIDD) that suffered from cervical spondylosis myelopathy, who had received anterior cervical discectomy and fusion (ACDF). CE specimens of healthy subjects were obtained from patients with a cervical fracture who received ACDF at The Second Affiliated Hospital of Nanchang University (Nanchang, China) and adopted SBC human ceRNA array V1.0（4×180K）. The results revealed that expressions of369 lncRNAs, 246 mRNAs, 578 circRNAs were different between degenerated cartilage endplate and healthy cartilage endplate. The functions of differentially expressed lncRNAs and co-expressed potential targeting genes were predicted by analyzing Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis. Furthermore, we analyzed and find the co-expression and interaction patterns of different RNAs and possible ceRNA mechanism. The present study provided a systematic perspective on the potential function of non-coding RNAs (ncRNAs) in the degeneration of cartilage endplate in CIDD.

2020-07-04 | GSE153761 | GEO

Human adipose tissue-derived mesenchymal progenitor cells induced toward adipogenic, chondrogenic, or osteogenic induction fates for 3 days.

Project description:The study aims to identify early osteogenic and chondrogenic lineage markers with time course bulk RNA-seq profiling of 3-day differentiation induced cells.

2023-04-01 | GSE204847 | GEO

RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-derived Stromal Stem Cells

Project description:Background: Tissue regeneration and recovery in the adult body depends on self-renewal and differentiation of stem and progenitor cells. Mesenchymal stem cells (MSCs) that have the ability to differentiate into various cell types, have been isolated from the stromal fraction of virtually all tissues. However, little is known about the true identity of MSCs. MSC populations exhibit great tissue-, location- and patient-specific variation in gene expression and are heterogeneous in cell composition. Methodology/Principal findings: Our aim was to analyze the dynamics of differentiation of two closely related stromal cell types, adipose tissue-derived MSCs and dermal fibroblasts (FBs) along adipogenic, osteogenic and chondrogenic lineages using multiplex RNA-seq technology. We found that undifferentiated donor-matched MSCs and FBs are distinct populations that stay different upon differentiation into adipocytes, osteoblasts and chondrocytes. The changes in lineage-specific gene expression occur early in differentiation and persist over time in both MSCs and FBs. Further, MSCs and FBs exhibit similar dynamics of adipogenic and osteogenic differentiation but different dynamics of chondrogenic differentiation. Conclusion: Our findings suggest that stromal stem cells including adipose-derived MSCs and dermal FBs exploit different molecular mechanisms of differentiation to reach a common cell fate. The early mechanisms of differentiation are lineage-specific and are similar for adipogenic and osteogenic differentiation but are distinct for chondrogenic differentiation between MSCs and FBs. A total of 91 samples were analyzed by multiplex RNA-seq. Samples represented replicates from two patients, two cell types and three differentiation protocols, as indicated by the sample annotation. 5 barcodes were unused, but the corresponding FASTQ files are included for completeness.

2012-06-27 | E-GEOD-37521 | biostudies-arrayexpress

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