Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl Mouse Molar Transcriptomes

ABSTRACT: Purpose: To study the function of Runx2 on mouse tooth root development. The goals of this study are to compare NGS-derived molar transcriptome profiling (RNA-seq) bwtween Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice to identify the potential downstream target of Runx2. Methods: molar mRNA profiles from PN7.5 Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice (induction at PN3.5) were generated by deep sequencing, using Novaseq. Results: Using an optimized data analysis workflow, we mapped about 68 million sequence reads per sample to the mouse genome ( mm10) and identified 80,214 transcripts with Partek E/M workflow. 427 differentially regulated genes were identified (＞1.8-fold, p＜0.05), of which 219 were upregulated and 208 were downregulated.

ORGANISM(S): Mus musculus

PROVIDER: GSE151562 | GEO | 2020/08/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl Incisor Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived incisor transcriptome profiling (RNA-seq) between Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice to identify the potential target of Runx2. Methods: Incisor mRNA profiles from one week after induction of one-month-old Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500. Results: Using an optimized data analysis workflow, we mapped about 68 million sequence reads per sample to the mouse genome ( mm10) and identified 80,214 transcripts in th incisors of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice with Partek E/M workflow. Five hundred and eleven differentially regulated genes were identified (＞2-fold, p＜0.05), of which 299 were upregulated and 212 were downregulated.

2020-03-05 | GSE146332 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl Mouse Molar Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl Mouse Molar Transcriptomes

| PRJNA636368 | ENA

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) assess genome-wide chromatin accessibility of Runx2fl/fl Mouse Molar Transcriptomes

Project description:Purpose: To study the function of Runx2 on mouse tooth root development. The goals of this study are to assess genome-wide chromatin accessibility of Runx2fl/fl Mouse Molar Transcriptomes to identify the potential downstream target of Runx2. Methods: the apical halves of lower 1st molars of PN7.5 control mice were lysed to get a single cell suspension. 50000 cells 50,000 cells were lysed, and followed by transposition reaction and purification, and PCR amplification. The library construction and sequencing were performed by NextSeq 500 platform.

2020-08-31 | GSE151563 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl Incisor Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl Incisor Transcriptomes

| PRJNA610172 | ENA

Single-cell RNAseq analysis of Gli1-GFP+ tooth roor progenitor cells and PTHrP+ dental follicle cells of the murine molar

Project description:A single cell transcriptional profile of both epithelial and mesenchymal cells in the tooth bud of the murine molar marked by Gli1-GFP+ tooth root progenitor cells or PTHrP+ dental follicle cells at postnatal day 6 (P6)

2023-07-19 | GSE237439 | GEO

RNA-seq of Runx2 cKO primary chondrocytes.

Project description:Purpose: To demonstrate Runx2's association with organizing the extracellular matrix in primary chondrocytes. Method: RNA samples were collected from primary chondrocytes of 5-day-old Col2a1-CreERT2;Runx2fl/fl and Runx2fl/fl mice, cultured with or without IL-1beta. Results: Thirty-three genes cultured without IL-1beta and 45 genes with IL-1beta were up- or down-regulated by more than 2-fold in the Runx2 knockout in primary chondrocytes. Conclusions: Genes including collagen fibers were down-regulated in Runx2 cKO primary chondrocytes.

2021-01-21 | GSE165084 | GEO

Stool-derived 16s rRNA V4 sequencing from inducible intestinal-epithelium-LSD1-cKO mice (Villin-CreERT2+ Lsd1fl/fl (icKO)) against WT (Villin-CreERT2+ Lsd1fl/+ (icKO)) controls (before and 1-6 weeks after tamoxifen treatment)

Project description:Upon tamoxifen induced recombination, Villin-CreERT2+ Lsd1fl/fl (icKO) mice develop an immature intestinal epithelium characterized by an incomplete differentiation of enterocytes and secretory lineages, reduced number of goblet cells and a complete loss of Paneth cells. The main goal of this experiment was to test whether maturation of intestinal epithelium affects microbiota establishment and development. In addition, this loss of differentiated cell types after Lsd1 recombination is gradual and dependent on renewal times of each specific cell type (i.e. enterocytes take less than a week to be fully replenished while Paneth cells cycle around every 4 weeks). Hence by collecting stool from the same mouse at different time points after tamoxifen induced recombination a relationship between loss of particular cell types and changes in bacterial populations can be established. In addition, we wanted to test whether maturation of intestinal epithelium affects microbiota establishment and development

2023-10-31 | E-MTAB-12626 | biostudies-arrayexpress

RNA-Seq in pancreatic islets isolated from Arid1aFl/Fl control and Arid1aFl/Fl; UBC-CreERT2 mice (Arid1a KO) with/without pancreatectomy.

Project description:RNA-Seq in pancreatic islets isolated from Arid1aFl/Fl control and Arid1aFl/Fl; UBC-CreERT2 mice (Arid1a KO) with/without pancreatectomy.

| PRJNA818717 | ENA

RNA-Seq in pancreatic islets isolated from Arid1aFl/Fl control and Arid1aFl/Fl; UBC-CreERT2 mice (Arid1a KO) with/without pancreatectomy

Project description:RNA-Seq in pancreatic islets isolated from Arid1aFl/Fl control and Arid1aFl/Fl; UBC-CreERT2 mice (Arid1a KO) with/without pancreatectomy

| PRJNA827844 | ENA

IGF1 treatment of developing mouse molar

Project description:When evolution leads to differences in body size, organs generally scale along. A well-known example of the tight relationship between organ and body size is the scaling of mammalian molar teeth. To investigate how teeth scale during development and evolution, we compared mouse and rat molar development from initiation through final size. Whereas the linear dimensions of the rat first lower molar are twice that of the mouse molar, their shapes are largely the same. We found that scaling of the molars starts early, and that the rat molar is patterned equally as fast but in a larger size than the mouse molar. Using transcriptomics, we discovered that a known regulator of body size, insulin-like growth factor 1 (Igf1), is more highly expressed in the rat molars compared to the mouse molars. Ex vivo and in vivo mouse models demonstrated that modulation of the IGF pathway reproduces several aspects of the observed scaling process. Furthermore, analysis of IGF1-treated mouse molars and computational modeling indicate that IGF signalling scales teeth by simultaneously inhibiting the cusp patterning programme and by enhancing growth, thereby providing a relatively simple mechanism for scaling teeth during development and evolution. Finally, comparative data from shrews to elephants suggest that this scaling of patterning mechanism regulates the minimum tooth size possible, as well as the patterning potential of large teeth.

2022-11-19 | GSE218338 | GEO

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