Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential LncRNA/mRNA expression profiling and functional network analyses in BMP2 deletion of mouse dental papilla cells

ABSTRACT: We examined the transcriptional changes of the dental papilla mesenchymal cells of Bmp2 floxed/floxed and knock out mice by performing global transcriptome analysis. Total RNAs were isolated from the Bmp2 floxed/floxed and knock out cells for 8h, 48h and 72h and were utilized for RNA-seq. Our results showed that different gene expression of coding RNAs and non-coding RNAs was observed and involved in cell cycle, transcriptional regulation and developmentally relevant signaling pathways.

ORGANISM(S): Mus musculus

PROVIDER: GSE174429 | GEO | 2022/01/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A fine-tuned regulation of Bmp2 by Nodal/TGFβ signalling induced lncRNA-Smad7

Project description:The transforming growth factor beta (TGF-β) superfamily proteins are potent regulators of cellular development and differentiation. Long non-coding RNAs (lncRNAs) play widespread roles in spatial-temporal regulation of early development. However, the roles of lncRNAs regulated by nodal/TGF-β signaling is still elusive. Here, we showed a nodal-driven Smad induced lncRNA in mouse embryonic stem cells (mESCs), lncRNA-Smad7, which is divergently transcribed to Smad7, regulates cell fate determination through repressing Bmp2. Depletion of lncRNA-Smad7 dramatically impairs cardiomyocyte differentiation in mESCs. Moreover, LncRNA-Smad7 represses Bmp2 expression and binds at the promoter region of Bmp2. Importantly, knock-down Bmp2 rescues the defect of cardiomyocyte differentiation. Hence, we showed that lncRNA-Smad7 is antagonistic to BMP signaling in mESCs. Furthermore, lncRNA-Smad7 regulates cell fate determination between osteocytes and myocytes formation in C2C12 cells by repressing Bmp2. Thus, we provide new insights regarding the antagonistic effects between nodal/TGF-β and BMP signaling via lncRNA-Smad7.

2022-10-19 | GSE178136 | GEO

Differential LncRNA/mRNA expression profiling and functional network analyses in BMP2 deletion of mouse dental papilla cells

Project description:Differential LncRNA/mRNA expression profiling and functional network analyses in BMP2 deletion of mouse dental papilla cells

| PRJNA729791 | ENA

Immortalized mouse floxed Bmp2 dental papilla mesenchymal cell lines preserve odontoblastic phenotype and respond to BMP2.

Project description:Bone morphogenetic protein 2 (Bmp2) is essential for odontogensis and dentin mineralization. Generation of floxed Bmp2 dental mesenchymal cell lines is a valuable application for studying the effects of Bmp2 on dental mesenchymal cell differentiation and its signaling pathways during dentinogenesis. Limitation of the primary culture of dental mesenchymal cells has led to the development of cell lines that serve as good surrogate models for the study of dental mesenchymal cell differentiation into odontoblasts and mineralization. In this study, we established and characterized immortalized mouse floxed Bmp2 dental papilla mesenchymal cell lines, which were isolated from 1st mouse mandibular molars at postnatal day 1 and immortalized with pSV40 and clonally selected. These transfected cell lines were characterized by RT-PCR, immunohistochemistry, and analyzed for alkaline phosphatase activity and mineralization nodule formation. One of these immortalized cell lines, iBmp2-dp, displayed a higher proliferation rate, but retained the genotypic and phenotypic characteristics similar to primary cells as determined by expression of tooth-specific markers as well as demonstrated the ability to differentiate and form mineralized nodules. In addition, iBmp2-dp cells were inducible and responded to BMP2 stimulation. Thus, we for the first time described the establishment of an immortalized mouse floxed Bmp2 dental papilla mesenchyma cell line that might be used for studying the mechanisms of dental cell differentiation and dentin mineralization mediated by Bmp2 and other growth factor signaling pathways.

| S-EPMC2980836 | biostudies-literature

Gene expression profiles of dental follicle cells after 7 days of differentiation in vitro with BMP2, IGF2 and dexamethasone

Project description:We analysed gene expression profiles in dental follicle cells after 7 days of osteogenic differentiation with different inducers. Total RNAs were isolated from dental follicle cells after 7 days of differentiation with dexamethasone, BMP2, IGF2 and for control with standard cell culture medium

2010-11-10 | E-GEOD-20963 | biostudies-arrayexpress

The human dental apical papilla promotes spinal cord repair through a paracrine mechanism

Project description:Traumatic spinal cord injury is an overwhelming condition that strongly and suddenly impacts the patient’s life and her/his entourage. There are currently no predictable treatments to repair the spinal cord, while many strategies are proposed and evaluated by researchers throughout the world. One of the most promising avenues is the transplantation of stem cells, although its therapeutic efficiency is limited by several factors, among which cell survival at the lesion site. In our previous study, we showed that the implantation of a human dental apical papilla, residence of stem cells of the apical papilla (SCAP), supported functional recovery in a rat model of spinal cord hemisection.

2021-12-20 | GSE191140 | GEO

Comparative gene expression profiles of dental follicleand and papilla tissues at E17 and PN2

Project description:The aim of this study was to determine the differences in dental follicle and papilla tissues of mouse first lower molar between E17 and PN2 at the molecular level by combinational use of laser microdissection and microarray. Two-condition experiment

2017-03-30 | GSE97180 | GEO

Expression data from human dental follicle cells

Project description:We analysed the genexpression of dental follicle cells (DFCs) after 3 days osteogenic differentiation with BMP2 after transfection with a DLX3 plasmid (pDLX3) and after transfection with an empty plasmid (pEV) Total RNAs were isolated from dental follicle cells after transfection with pDLX3 and pEV and osteogenic induction with BMP2 at day 3

2014-08-01 | E-GEOD-59949 | biostudies-arrayexpress

Transcription profiling of chicken histone H1 null mutant cells

Project description:In chicken DT40 cells, there are six linker histone H1 variants and 12 of coding genes. We have previously reported of 11 out of 12 H1 knock out DT40 cells (Takami et al., Genes to Cell 1997 [PMID:9491804]) but complete H1 null DT40 cells could not established, so far. We identified one of the H1 variant, H1R was involved in genomic instabilities (Hashimoto et al., DNA repair (2007) [17613284]), so we re-introduced floxed H1R-eGFP and mer-cre-mer into 11 out of 12 H1 knock out DT40 cells. Then we targeted last enedogenous H1, we successfully established conditional H1 KO cells (K11). Next we treated with tamoxifen to loop out floxed H1R-eGFP, and cloning H1 completely null cells (K11-5, and K11-7). We analysis those gene expression pattern in wild-type, K11, and K11-5 cells Experiment Overall Design: Apoptosis is induced in H1 null cells, so we inhibit apoptosis with pan-caspase inhibitor, Z-VAD-FMK and extract RNAs.

2008-11-04 | E-GEOD-8483 | biostudies-arrayexpress

Global profiling of human hair follicle scalp dermal papilla cells using Affymetrix microarrays

Project description:Dermal papilla cells isolated from the human hair follicle are capable of inducing hair growth in recipient epithelia. However, demonstrating disparity from rodent dermal papilla, human cells lose this inductive competance immediately upon growth in culture under normal growth conditions. We grew dermal papilla cells in hanging drop cultures that are morphologically akin to intact dermal papilla, and found that by enhancing the environment for aggregation, we could restore the inductive capacity of human dermal papilla cells in culture. The underlying genes that regulate the inductive potential of dermal papilla cells is not well understood, and we sought to use global profiling to identify key genes and pathways related to inductive competance within dermal papilla cells. We used Affymetrix microarrays to profile human dermal papilla cells in both hair inducing, and non-hair inducing states. Affymetrix microarrays were used to to perform profiling of human dermal papilla cells, both as intact tissues (freshly isolated from scalp), and at several stages in subsequent two dimensional culture; cell explant outgrowths (p0), cells at passage 1 (p1), passage 3 (p3) and passage 5 (p5). RNA was isolated from cultured cells 72 hours after feeding. Cells at passage 3 were also grown in hanging drops to form dermal spheroids, that were used for RNA collection 48 hours after establishment. All experiments were performed using tissue from three biological replicates (#D5, D6, D7),

2013-10-20 | E-GEOD-44765 | biostudies-arrayexpress

Differential lncRNA/mRNA Expression Profiling and Functional Network Analyses in Bmp2 Deletion of Mouse Dental Papilla Cells.

Project description:Bmp2 is essential for dentin development and formation. Bmp2 conditional knock-out (KO) mice display a similar tooth phenotype of dentinogenesis imperfecta (DGI). To elucidate a foundation for subsequent functional studies of cross talk between mRNAs and lncRNAs in Bmp2-mediated dentinogenesis, we investigated the profiling of lncRNAs and mRNAs using immortalized mouse dental Bmp2 flox/flox (iBmp2fx/fx) and Bmp2 knock-out (iBmp2ko/ko) papilla cells. RNA sequencing was implemented to study the expression of the lncRNAs and mRNAs. Quantitative real-time PCR (RT-qPCR) was used to validate expressions of lncRNAs and mRNAs. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict functions of differentially expressed genes (DEGs). Protein-protein interaction (PPI) and lncRNA-mRNA co-expression network were analyzed by using bioinformatics methods. As a result, a total of 22 differentially expressed lncRNAs (16 downregulated vs 6 upregulated) and 227 differentially expressed mRNAs (133 downregulated vs. 94 upregulated) were identified in the iBmp2ko/ko cells compared with those of the iBmp2fx/fx cells. RT-qPCR results showed significantly differential expressions of several lncRNAs and mRNAs which were consistent with the RNA-seq data. GO and KEGG analyses showed differentially expressed genes were closely related to cell differentiation, transcriptional regulation, and developmentally relevant signaling pathways. Moreover, network-based bioinformatics analysis depicted the co-expression network between lncRNAs and mRNAs regulated by Bmp2 in mouse dental papilla cells and symmetrically analyzed the effect of Bmp2 during dentinogenesis via coding and non-coding RNA signaling.

| S-EPMC8727545 | biostudies-literature

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