Comparative study of gene expression in lower and upper first molar cap stage tooth germs of DUHi and FVB mice
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA558890 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9908500.fastq.gz | Fastqsanger.gz | |||
| SRR9908501.fastq.gz | Fastqsanger.gz | |||
| SRR9908502.fastq.gz | Fastqsanger.gz | |||
| SRR9908493.fastq.gz | Fastqsanger.gz | |||
| SRR9908503.fastq.gz | Fastqsanger.gz |
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Project description:The dataset aims at comparing gene expression in the developing lower and upper first molars of two mouse strains: DUHi and FVB. We studied molar tooth germ an early cap stage, looking for differences in activation-inhibition mechanisms that promote tooth formation. 19202 genes are in common between FVB and reference strain C57B6 and have a MGI annotation. Out of these genes, 2234 genes (11.6%) presented a significant difference of expression between the mapping on the reference strain C57B6 and the mapping on FVB strain (DESeq2, adjusted P value < 0.05, considering the mapping effect that is with 12 replicates). This is presumably a mapping artifact, due to the sequence divergence between mouse strains. These genes were removed, and the remaining 16,968 genes were retained for further analysis. 3619 genes were found to be differentially expressed between the two strains in the lower and upper molar (jaw+strain)
2020-03-27 | GSE135432 | GEO
Project description:Numerous genes that play important regulative roles during tooth development in mice have been identified. However, very little is known about gene expression and function in human odontogenesis. We used microarrays to detail the global programme of gene expression underlying tooth development and identified distinct classes of up-regulated genes during in the tooth germs. Tooth germs of molar, incisor, and canine at the cap stage were dissected, respectively, from 12-week-old human embryonic oral cavity for RNA extraction and hybridization on Affymetrix microarrays. We sought to screen for the genes that are strongly expressed in the dental tissues and analysis if these genes related to mammalian tooth development and tooth abnormalities.
2015-04-01 | E-GEOD-48150 | biostudies-arrayexpress
Project description:Transcriptional profiling of mouse E14 tooth molar germ comparing E11, 12, 16, 18 tooth molar germ. Goal was to identify unknown genes involved in tooth development,
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Project description:Dioxins are ubiquitous environmental poisons that are developmentally toxic. Exposure of mouse E14 tooth germs to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) leads to reduced tooth size and deformation of cuspal morphology implying the induction of a variety of biological responses on both cellular and molecular levels. To verify such responses at the gene level, mouse embryonic cap staged tooth germs were cultured for 24 h with/without 1 µM TCDD. Keywords: tissue culture, exposure to TCDD, tooth development
2006-08-19 | GSE4873 | GEO
Project description:miRNAs are not well known their expression and function in tooth development. To identify the miRNAs expression during tooth development, tooth germs were dissected from the initiation bud, cap and bell stages. miRNA-chip expression analysis was performed with RNAs of the molar tooth germs from embryos of pregnant mice at emrbryonic day 11, 12, 14, and 16, using Agilent's miRNA microarray.
2014-01-09 | E-GEOD-53903 | biostudies-arrayexpress
Project description:Previous studies have suggested that Bmp4 is a key Msx1-dependent mesenchymal odontogenic signal for driving tooth morphogenesis through the bud-to-cap transition. Whereas the bud stage tooth developmental arrest in Msx1-/- mutant mice was accompanied by reduction in mesenchymal Bmp4 mRNA expression, we show that depleting functional Bmp4 mRNAs in the tooth mesenchyme, through neural crest-specific gene inactivation in Bmp4f/f;Wnt1Cre mice, caused mandibular molar developmental arrest at the bud stage but allowed maxillary molars and incisors to develop to mineralized teeth. We show that the Wnt inhibitors Dkk2 and Wif1 were much more abundantly expressed in the mandibular than maxillary molar mesenchyme in wildtype embryos and that Dkk2 expression was significantly unregulated in the tooth mesenchyme in Bmp4f/f;Wnt1Cre embryos. In addition, expression of Osr2, which encodes a zinc finger protein that antagonizes Msx1-mediated activation of odontogenic mesenchyme, is significantly upregulated in the molar mesenchyme in Bmp4f/f;Wnt1Cre embryos. Msx1 heterozygosity enhanced maxillary molar developmental defects whereas Osr2 heterozygosity rescued mandibular first molar morphogenesis in Bmp4f/f;Wnt1Cre mice. Moreover, in contrast to complete lack of supernumerary tooth initiation in Msx1-/-Osr2-/- mutant mice, Osr2-/-Bmp4f/f;Wnt1Cre compound mutant mice exhibit formation and subsequent arrest of supernumerary tooth germs that correlated with down regulation of Msx1 expression in the tooth mesenchyme. Taken together, our data indicate that, while reduction in mesenchymal Bmp4 expression alone could not account for the tooth bud arrest phenotype in Msx1-/- mutant mice, Bmp4 signaling synergizes with Msx1 and antagonizes Osr2 to activate mesenchymal odontogenic activity to drive tooth morphogenesis and sequential tooth formation. E13.5 mouse embryos tooth germs were microdissected by laser capture microdissection (LCM), and the mandibular molar and maxillary molar were separated. 3 pairs of control and mutant samples were pooled for the RNA extraction.
2013-01-22 | E-GEOD-39918 | biostudies-arrayexpress
Project description:Embryologically the tooth is derived from both the ectoderm and neural crest (ectomesenchyme). It is often used as a model to study how epithelialmesenchymal interactions can control differentiation and morphogenesis. During early development organs of ectodermal origin share both a set of signalling molecules and exhibit common morphological features, subsequently proceeding along separate developmental programs.<br><br>Tooth development is a continuous process that can be divided into the initiation -, bud -, cap -, and bell-stages. In mice, tooth development begins at embryonic day 11.5 (E11.5), by thickening of the dental epithelium, while mineralization of enamel and dentin in first molar starts at postnatal day 0 (P0) (5). A multistep and complex process of the gene expression are involved in the early stage of tooth development. So far expression of more than 1300 genes and/or proteins have been detected during tooth germ development by microarrays/immunocytochemistry/in situ hybridization. Studies with mutant mice have identified a number of genes that regulate tooth development and morphology. For example, deficiency of Lef-1 or P63 arrests tooth development at early stages. Deficiency of Msx1 or Pax9 results in arrest of tooth development at the bud stage , while deficiency of Runx2/Cbfa1 or Sp3 inhibits cyto-differentiation of ameloblasts and/or odontoblasts. Shh is required for normal growth and morphogenesis, but is not essential for cyto-differentiation of the ameloblast and odontoblast populations. Ameloblastin and amelogenin knock-out mice develop severe enamel hypoplasia with abnormal ameloblast differentiation. <br><br>Recently, new connections between retinoid metabolism and PPAR responses have been identified. It has also been shown that endogenous retinoic acid is necessary for the initiation of odontogenesis , and that some of the genes that catalyze the oxidation of retinaldehyde into retinoic acid, exhibit distinct patterns of expression in developing murine teeth. Little is known about functions of PPAR-a as regards tooth germs or mature teeth. It is, however, likely that mitochondrial oxidative metabolism well as fatty acid metabolism is enhanced in late odontogenesis. These are metabolic activities which in other tissues are stimulated by PPAR-a agonists.<br><br>For this reason it was of interest to carry out comparative gene expression profiling of the first molar tooth germs of PPAR-a knock-out mouse and of the corresponding wild-type mice. The results suggest marked differences in gene expression, parts of which may be associated with an observed hypomineralization of enamel in the mature PPAR-a knock-out murine tooth.
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Project description:To identify genes heretofore undiscovered as critical players in the biogenesis of teeth, we have used microarray gene expression analysis of the developing mouse molar tooth (DMT) between 1 and 10 days postnatal to identify genes differentially expressed when compared to 16 control tissues (GEO accession # GSE1986). Of the top 100 genes exhibiting increased expression in the DMT, 29 were found to have been previously associated with tooth development. Differential expression of the remaining 71 genes not previously associated with tooth development was confirmed by qRT-PCR analysis. Further analysis of seven of the latter genes by mRNA in situ hybridization found that five were specific to the developing tooth in the craniofacial region (Rspo4, Papln, Amtn, Gja1, Maf). Of the remaining two, one was found to be more widely expressed (Sp7) and the other was found to be specific to the nasal serous gland, which is close to, but distinct from, the developing tooth (Vrm). Experiment Overall Design: mRNA from molar teeth extracted from Swiss Webster mouse pups between 1 and 10 days post-natal was pooled, labeled, and hybridized in quadruplicate to Affymetrix Mouse Genome Expression 430 2.0 microarrays. This data was compared to that of 16 control tissues (GEO accession # GSE1986) to identify genes differentially expressed in the DMT mRNA.
2008-06-15 | E-GEOD-7164 | biostudies-arrayexpress
Project description:Organoid models provide powerful tools to study tissue biology and development in a dish. Here, we established first-time organoid models from early-postnatal (postnatal day 7) mouse molar and incisor, capable of differentiation toward ameloblast-like cells in vitro. To more in detail characterise organoids from mouse molar and incisor, bulk RNA-sequencing was performed on the following (1) early passage (passage 0) organoids from both tooth types grown in basal tooth organoid medium (TOM) with or without addition of exogenous epidermal growth factor (EGF); and (2) late passage (passage 5) organoids grown in TOM+EGF or differentiation medium (DM).
2023-04-19 | E-MTAB-12557 | biostudies-arrayexpress
Project description:Throughout the various stages of tooth development, reciprocal epithelial-mesenchymal interactions are the driving force, for instance crucially involved in the differentiation of mature enamel-forming ameloblasts and dentin-producing odontoblasts. Here we established mouse tooth ‘assembloids’, comprised of tooth organoid-derived dental epithelial cells (from mouse molars and incisors) cultured together with molar dental pulp stem cells (DPSCs), to mimic these developmental interactions. Assembloids from both tooth types were grown both in basal- and differentiation-inducing conditions. Single cell transcriptomics analysis was applied to in detail characterize and validate the newly developed mouse tooth assembloid model and evaluate the induced differentiation processes.
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