Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from human dental pulp stem cells and bone marrow mesenchymal stem cells

ABSTRACT: To further reveal the mechanism of the senescence resistant property of mesenchymal stem cells from human, a gene expression profiling approach was used to compare the functional gene expression changes in BMMSCs and DPSCs with Affymetrix GeneChip Human Gene 1.0 ST arrays analysis. Using bioinformatic analysis, we aimed to identify changes in genes and pathways in human DPSCs and BMMSCs . Cells (BMMSCs and DPSCs) from healthy male subjects were seeded in 10 cm2 dishes and cultured until they reached 80 % confluence, and total RNA of DPSCs and BMMSCs were extracted and analyzed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE217636 | GEO | 2022/11/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Bone marrow-derived and dental pulp-derived human mesenchymal stem cell RNA-Seq

Project description:Lineage commitment and tumorigenesis specify adult stem cells from different tissues or organs. To gain insight into the mechanism of this programming, phenotypic, functional and transcriptome analyses were performed in mesenchymal stem cells derived from human dental pulp (DPSCs) and bone marrow (BMSCs). DPSCs and BMSCs had similar morphologies and flow cytometric profiles, and were capable of tri-lineage differentiation into osteoblast, adipocyte and chondocyte. However, compared with BMSCs, DPSCs increased in osteogenic potential, decreased in adipogenic potential, and formed dentin-pulp-like complexes in vivo. Genome-wide RNA-seq and differential expression analysis revealed that signalings such as, phosphatase and tensin homolog (PTEN)/PI3K/AKT pathway, and cancer-related pathway were different in both cells. Differential PTEN expression, higher in DPSCs than BMSCs, was responsible for the lineage commitment and tumorigenesis differences in both cells. Besides, BMSCs decreased in PTEN DNA methylation compared to DPSCs, which was mediated by increased DNA (cytosine-5) methyltransferase 3B (DNMT3B) expression. Furthermore, histone methyltransferase G9a mediated repressive epigenetic mark H3K9Me2 was selectively enriched in BMSCs. Moreover, DPSCs were more resistant to oncogenic transformation than BMSCs. To link lineage commitment with tumorigenesis, we demonstrated that DPSCs were more resistant to oncogenic transformation than BMSCs and PTEN deficiency increased the sensitivity of DPSCs for tumorigenic transformation. The results help understanding the roles of the epigenetic factors in lineage commitment and tumorigenesis and also for therapeutic uses of adult stem cells.

2019-03-17 | GSE105145 | GEO

Identification of mirna during osteoblast differentiation of human dental pulp stem cells

Project description:To evaluate the miRNA and mRNA expression profiles (miRNOME) we identified miRNAs during in vitro osteogenic differentiation of human dental pulp stem cells (DPSC). The DPSCs were cultured in the DMEM + beta-glycerol phosphate, ascorbic acid and dexamethasone for 2 dias to 21days. The microRNA or mRNA expression profiling during the differentiation process was analyzed through hybridizations with Agilent miRNA-microarray (8x15K format).

2014-11-28 | E-MTAB-3077 | biostudies-arrayexpress

Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns.

Project description:Early embryonic stages of pluripotency are modeled for epigenomic studies primarily with human embryonic stem cells (ESC) or induced pluripotent stem cells (iPSCs). For analysis of DNA methylation, however, ESCs and iPSCs do not accurately reflect the DNA methylation levels found in preimplantation embryos. Whole genome bisulfite sequencing (WGBS) approaches have revealed the presence of large partially methylated domains (PMDs) covering 30-40% of the genome in oocytes, preimplantation embryos, and placenta. In contrast, ESCs and iPSCs show abnormally high levels of DNA methylation compared to inner cell mass (ICM) or placenta. Here we show that dental pulp stem cells (DPSCs), derived from baby teeth and cultured in serum-containing media, have PMDs and mimic the ICM and placental methylome more closely than iPSCs and ESCs. By principal component analysis, DPSC methylation patterns were more similar to two other neural stem cell types of human derivation (EPI-NCSC and LUHMES) and placenta than were iPSCs, ESCs or other human cell lines (SH-SY5Y, B lymphoblast, IMR90). To test the suitability of DPSCs in modeling epigenetic differences associated with disease, we compared methylation patterns of DPSCs derived from children with chromosome 15q11.2-q13.3 maternal duplication (Dup15q) to controls. Differential methylation region (DMR) analyses revealed the expected Dup15q hypermethylation at the imprinting control region, as well as hypomethylation over SNORD116, and novel DMRs over 147 genes, including several autism candidate genes. Together these data suggest that DPSCs may be useful model for epigenomic and functional studies of human neurodevelopmental disorders.

2017-09-20 | GSE93134 | GEO

Proteomic Analysis of dental pulp stem cell-derived exosomes

Project description:In order to examine the proteomics of exosomes derived from DPSCs under hypoxia (Hypo-Exos) and the mechanism underlying the angiogenic effect of DPSC-Exos, iTRAQ-based proteomics analysis and bioinformatic analysis were performed to investigate proteome profile differences between exosomes derived from DPSCs under normoxia (Nor-Exos) and Hypo-Exos.7114 peptides and 1792 proteins were identified from the Hypo-Exos samples with a 1% FDR. Compared with the control group, 39 proteins were upregulated and 40 proteins were downregulated in Hypo-Exos.

2022-05-20 | PXD032719 | Pride

Development of gene expression signatures for SOX2 overexpressing human dental pulp stem cells

Project description:As a key factor for cell pluripotent and self-renewing phenotypes, SOX2 has attracted scientists’ attention gradually in recent years. However, its exact effects in dental pulp stem cells (DPSCs) are still unclear. In this study, we mainly investigated whether SOX2 could affect some biological functions of DPSCs.

2015-09-30 | GSE73548 | GEO

Transcriptomic analysis of ETV2-overexpressing human dental pulp stem cells

Project description:To better understand the global responses of DPSCs to ETV2 overexpression after osteogenic induction, we performed a genome-wide transcriptome analysis by RNA-sequencing technology to determine the global changes on gene expression level

2022-10-12 | GSE160451 | GEO

Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [ATAC-seq]

Project description:Chromatin accessibility is key epigenomic regulatory mechanisms of transcription. Herein, to profile open chromatin maps and transcriptional feature associated with odontogenic tropism of dental pulp stem cells (DPSCs), we conducted integrative analysis of epigenomic alteration and transcriptome changes during odontogenic differentiation of DPSCs. DPSCs were long-term cultured in odontogenic induction medium to evaluate differentiation abilities. ATAC-seq and RNA-seq samples were collected before and after the 9-day culture. One of the day 9 specific-super-enhancer was constructed in ALPL (Alkaline Phosphatase, Biomineralization Associated) intragenic region in which all the day 9-specific open chromatin peaks were included and BMP-mediated Smad binding element are specifically accumulated. These results suggest that the specific local chromatin regions were selectively opened and, particularly, super-enhancers were constructed, which was able to guide differentiative transcriptional factors such as Smad1/4 to their target gene loci in differentiating DPSCs; hence, epigenetic modifications such as histone deacetylase (HDACs) inhibitor application have therapeutic potential for DPSCs-induced dentin/pulp regeneration.

2023-09-29 | GSE244058 | GEO

Integrative epigenomic and transcriptomic anlaysis of odontogenic differentiation of dental pulp stem cells [RNA-seq]

2023-09-29 | GSE244057 | GEO

Identification of netwoks mirna-mrna interactions during osteoblast differentiation of human dental pulp stem cells

Project description:To evaluate the miRNA and mRNA expression profiles (miRNOME and transcriptome) we reconstructed networks identifying miRNAs and mRNA during in vitro osteogenic differentiation of human dental pulp stem cells (DPSC). The DPSCs were cultured in the DMEM + beta-glycerol phosphate, ascorbic acid and dexamethasone for 2 to 21 days. The microRNA or mRNA expression profiling during the differentiation process was analyzed through hybridizations with Agilent miRNA-microarray (8x15K format) or whole-human genome Agilent microarray (4x44K format).

2014-11-13 | E-MTAB-3010 | biostudies-arrayexpress

The proteomics analysis of ETV2-overexpressing dental pulp stem cells

Project description:DPSCs derivedgenerated from the three different donors were transfectedinfected with ETV2-overexpressing lentiviralrus particles or control lentiviralus particles. Protein samples were harvested after 10 days of endothelial differentiation. Proteome profiling was performed by the iProteome platform of the Fudan University Human Phenome Institute according to user guide.

2020-03-21 | PXD018138 | iProX

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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