DEVELOPMENTAL MicroRNA EXPRESSION PROFILING OF MURINE EMBRYONIC OROFACIAL TISSUE
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PROVIDER: PRJNA124719 | ENA |
REPOSITORIES: ENA
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Project description:BACKGROUND: Orofacial development is a multifaceted process involving precise, spatio-temporal expression of a panoply of genes. MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing, and represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. RESULTS: To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) -12, -13 and -14 murine orofacial tissue were compared utilizing miRXplore™ microarrays from Miltenyi Biotech GmbH. TaqManTM quantitative Real-Time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA (hierarchical) clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. Expression of over 26% of the approximately 588 murine miRNA genes examined was detected in murine orofacial tissues from GD 12, 13 and 14. Among these expressed genes several clusters were seen to be developmentally regulated. Differential expression of genes encoding miRNAs within such clusters were shown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial-mesenchymal transformation, all processes critical for normal orofacial development. Functional relationships between miRNAs differentially expressed were investigated using Ingenuity Pathway Analysis (IPA; Ingenuity Systems). CONCLUSIONS: Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein-encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs. Time-course experiment (Developmental Stages), ICR mice embryos on gestational days (GD) 12, 13 and 14. Biological replicates: For each day of gestation, 3 independent pools of 15 to 20 staged embryos were used to procure embryonic orofacial tissues for preparation of 3 distinct pools of RNA that were independently processed and applied to individual miRXplore™ microRNA Microarray chips (Miltenyi Biotec GmbH). Technology: 2-color spotted cDNA, Hy5 (experimental sample) vs. Hy3 (control - miRXplore Universal Reference).
2010-12-01 | E-GEOD-20880 | biostudies-arrayexpress
Project description:BACKGROUND: Orofacial development is a multifaceted process involving precise, spatio-temporal expression of a panoply of genes. MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing, and represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. RESULTS: To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) -12, -13 and -14 murine orofacial tissue were compared utilizing miRXplore™ microarrays from Miltenyi Biotech GmbH. TaqManTM quantitative Real-Time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA (hierarchical) clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. Expression of over 26% of the approximately 588 murine miRNA genes examined was detected in murine orofacial tissues from GD 12, 13 and 14. Among these expressed genes several clusters were seen to be developmentally regulated. Differential expression of genes encoding miRNAs within such clusters were shown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial-mesenchymal transformation, all processes critical for normal orofacial development. Functional relationships between miRNAs differentially expressed were investigated using Ingenuity Pathway Analysis (IPA; Ingenuity Systems). CONCLUSIONS: Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein-encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs.
2010-12-01 | GSE20880 | GEO
Project description:Developmental gene expression profiling of mammalian, fetal orofacial tissue Keywords = orofacial Keywords = embryo Keywords = development Keywords: time-course
2004-08-03 | GSE1624 | GEO
Project description:BackgroundOrofacial development is a multifaceted process involving precise, spatio-temporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs involved in gene silencing, represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development.MethodsTo identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) -12, -13 and -14 murine orofacial tissue were compared utilizing miRXplore microarrays from Miltenyi Biotech. Quantitative real-time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis.ResultsExpression of over 26% of the 588 murine miRNA genes examined was detected in murine orofacial tissues from GD-12-GD-14. Among these expressed genes, several clusters were seen to be developmentally regulated. Differential expression of miRNAs within such clusters wereshown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial-mesenchymal transformation, all processes critical for normal orofacial development.ConclusionsUsing miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein-encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs.
| S-EPMC3146018 | biostudies-literature
Project description:DEVELOPMENTAL MicroRNA EXPRESSION PROFILING OF MURINE NEURAL TUBE
| PRJNA124717 | ENA
Project description:BACKGROUND: Development of the neural tube is a highly orchestrated process relying on precise, spatio-temporal expression of numerous genes as well as hierarchies of signal transduction and gene regulatory networks. Disruption of expression of a number of genes participating in these networks is believed to underlie developmental anomalies such as neural tube defects (NTDs) resulting from anomalous neural tube morphogenesis. MicroRNAs (miRNAs), a large family of noncoding RNAs, have been shown to function as gene silencers, and thus, are key modulators of cell and tissue differentiation. To elucidate potential roles of miRNAs in murine neural tube development, miRNA gene expression profiling has been utilized in the current study, to garner novel and in-depth knowledge on the expression and regulation of genes encoding miRNAs as well as their potential target genes governing maturation of the mammalian neural tube. METHODS: With the aim of identifying differentially expressed miRNAs during mammalian neural tube ontogenesis, miRNA expression profiles from gestation day (GD) -8.5, -9.0 and -9.5 murine neural tube tissue were compared utilizing miRXplore™ microarrays from Miltenyi Biotech GmbH. Gene expression changes observed in microarray analysis were verified by TaqManTM quantitative Real-Time PCR. clValid R package and the UPGMA (hierarchical) clustering method were utilized for cluster analysis of the microarray data. Functional associations among selected miRNAs were examined exploiting Ingenuity Pathway Analysis. RESULTS: Expression of approximately 12% of the 609 murine miRNA genes examined was detected in murine neural tube tissues from GD -8.5, -9.0 and -9.5. Clustering analysis revealed several developmentally regulated clusters among these expressed genes. MicroRNA target analysis enabled identification of a panoply of protein-coding target genes of the differentially expressed miRNAs within such clusters. Interestingly, many of these target genes have been shown to be associated with vital cellular processes such as cell proliferation, cell adhesion, cell migration, differentiation, apoptosis and epithelial-mesenchymal transformation, all of which are essential for normal neural tube development. Utilization of Ingenuity Pathway Analysis (IPA; Ingenuity Systems) allowed identification of interactive biological networks connecting differentially expressed miRNAs and their target genes highlighting functional relationships. CONCLUSIONS: In the present study, a unique gene expression signature of a range of miRNAs in embryonic neural tube tissue was delineated. Analysis of miRNA target genes and gene interaction pathways emphasized that expression of numerous protein-encoding genes, indispensable for normal neural tube morphogenesis, may be regulated by specific miRNAs. Time-course experiment (Developmental Stages), ICR mice embryos on gestational days (GD) 8.5, 9.0 and 9.5. Biological replicates: For each day of gestation, 3 independent pools of 15 to 20 staged embryos were used to procure embryonic orofacial tissues for preparation of 3 distinct pools of RNA that were independently processed and applied to individual miRXplore™ microRNA Microarray chips (Miltenyi Biotec GmbH). Technology: 2-color spotted cDNA, Hy5 (experimental sample) vs. Hy3 (control - miRXplore Universal Reference).
2010-12-01 | E-GEOD-20879 | biostudies-arrayexpress
Project description:Developmental gene expression profiling of mammalian, fetal orofacial tissue
2007-10-12 | E-GEOD-1624 | biostudies-arrayexpress
Project description:RNA methylation destabilizes developmental regulators in murine embryonic stem cells
| PRJNA202906 | ENA
Project description:The noncoding genome contains sequences called enhancers which facilitate expression of target genes through recruitment and binding of transcription factors. Enhancers are typically active in developmental stage-, tissue-, and cell type-specific patterns, whereby they control the spatiotemporal expression patterns of target genes. Sequence variation within enhancers can alter expression of their target genes where the enhancer is active, causing isolated phenotypes ranging from normal morphological differences to malformations. The role of orofacial enhancers in normal morphology and disease of the orofacial region has previously been established in bulk human assays. However, the conservation of these findings and the cell types contributing to these phenotypes are unknown, limiting work in prevention and treatment of malformations. To uncover cell type-specific enhancers whose sequence variants contribute to normal facial morphology and malformations, we performed single cell multiome (snATAC and snRNA-seq) sequencing on 17 human samples spanning 6 unique stages from 4-8 weeks gestation and 14 mouse samples spanning 6 stages from E9.5-15.5. We identified 15 distinct cell types, for which we leveraged the cell type specific chromatin accessibility and transcriptomic profiles and previously published chromatin conformation data to identify cell type specific enhancer-gene predicted interactions, which we call the ‘enhancerprints’. These enhancerprints revealed a cell type-specific enrichment pattern of common single nucleotide variants for biologically relevant phenotypes such as epithelium in orofacial clefting and mesenchyme in facial variation.
2025-12-01 | GSE249497 | GEO
Project description:The noncoding genome contains sequences called enhancers which facilitate expression of target genes through recruitment and binding of transcription factors. Enhancers are typically active in developmental stage-, tissue-, and cell type-specific patterns, whereby they control the spatiotemporal expression patterns of target genes. Sequence variation within enhancers can alter expression of their target genes where the enhancer is active, causing isolated phenotypes ranging from normal morphological differences to malformations. The role of orofacial enhancers in normal morphology and disease of the orofacial region has previously been established in bulk human assays. However, the conservation of these findings and the cell types contributing to these phenotypes are unknown, limiting work in prevention and treatment of malformations. To uncover cell type-specific enhancers whose sequence variants contribute to normal facial morphology and malformations, we performed single cell multiome (snATAC and snRNA-seq) sequencing on 17 human samples spanning 6 unique stages from 4-8 weeks gestation and 14 mouse samples spanning 6 stages from E9.5-15.5. We identified 15 distinct cell types, for which we leveraged the cell type specific chromatin accessibility and transcriptomic profiles and previously published chromatin conformation data to identify cell type specific enhancer-gene predicted interactions, which we call the ‘enhancerprints’. These enhancerprints revealed a cell type-specific enrichment pattern of common single nucleotide variants for biologically relevant phenotypes such as epithelium in orofacial clefting and mesenchyme in facial variation.
2025-12-01 | GSE249496 | GEO