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Next Generation Sequencing Facilitating Quantitative Analysis of Wild Type (Kcnj11fl/fl, WT) and β-cell Specific Kcnj11 -/- (βKcnj11 -/-, bKO) Mouse Islets' Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitating Quantitative Analysis of Wild Type (Kcnj11fl/fl, WT) and β-cell Specific Kcnj11 -/- (βKcnj11 -/-, bKO) Mouse Islets' Transcriptomes

PROVIDER: PRJNA660242 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitating Quantitative Analysis of Wild Type (Kcnj11fl/fl, WT) and β-cell Specific Kcnj11 -/- (βKcnj11 -/-, bKO) Mouse Islets' Transcriptomes

Project description:β-cell Specific Kcnj11 -/- mice and their islets exhibited a hirtherto unkown switch in the major signaling pathway of G-protein coulpled receptors from Gs to Gq, and overall enhanced Gq signaling. That the phenomeno was also observed in their isolated islets, and that the genetic manipulation of the mice was only in the pancreatic beta-cells, we reasoned that peharps knockout of Kcnj11 in beta cells could result to a general change in the expression of genes related to G-protein coupled receptor signaling. Since New-Generation Sequencing (NGS) has revolutionized cellular based pathway analysis, we extracted total RNA from WT and bKO islets, performed NGS and compared global changes in the expression of genes between WT and bKO islets.

2021-04-24 | GSE156917 | GEO

RNA sequencing in islets from Rip-Cre CDK8fl/fl and CDK8fl/fl mice with or without metabolic stress.

Project description:mRNA of pancreatic islets from Rip-Cre CDK8fl/fl and CDK8fl/fl mice were sequenced to investigate the consequence of genetic CDK8 ablation on genome wide transcript levels. Additionally, Rip-Cre CDK8fl/fl and CDK8fl/fl mice were stressed with STZ and then islets from those mice were sequenced to describe the transcriptome-wide regulation of beta-cells under stress condition.

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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: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.

2020-08-31 | GSE151562 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Reverb fl/fl and Reverb fl/fl /MHC+ cardiac Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Reverb fl/fl and Reverb fl/fl /MHC+ cardiac Transcriptomes

| PRJNA639127 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in fetal and 2 weeks old rat islets

Project description:Unlike adult β-cells, fetal and neonatal islets are functional immature and have blunted glucose responsiveness and decreased insulin secretion in response to stimuli. Pancreatic islets are a mixture of different cell types. Study of transcriptomes from intact islets would identify novel molecular mechanisms controlling islet functional development. At e19 and 2 weeks of age, pancreatic islets were isolated and total RNA were extracted for RNA-Seq study. Gene expression profiles were compared in the study.

2020-07-02 | GSE153604 | GEO

Next-generation sequencing facilitates quantitative analysis of wild type and diabetic db/db mice islets transcriptomes

Project description:Long non-coding RNAs (LncRNAs) constitute an extensive fraction of the mammalian transcriptome. In this study, lncRNAs dysregulated in the islets of diabetic db/db mice were identified by high-throughput RNA sequencing. More than 1600 lncRNAs were detected using RNA sequencing, indicating that lncRNAs were abundant in islets. Among them, we found that lncRNA-Malat1 was significantly reduced in diabetic mouse islets. Further experiments suggested an involvement of lncRNA-Malat1 in lipotoxicity-induced β-cell dysfunction.

2022-11-01 | GSE139823 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Elf4fl/fl-Villin-Cre Livers Transcriptomes

Project description:Conclusion: Elf4fl/fl-Villin-Cre mice are more sensitive to alcohol induced liver steatosis

2022-05-18 | GSE192923 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Uhrf1-/- fetal liver hematopoietic stem cell (FL-HSCs) Transcriptomes

Project description:To investigate the molecular mechanism of Uhrf1 in controlling the self-renewal versus differentiation of FL-HSCs, high-throughput sequencing was performed to analyze the transcriptomes of WT and Uhrf1-deficient FL-HSCs.Consistent with the erythroid-biased differentiation of Uhrf1-deficient FL-HSCs, genes involved in erythrocyte differentiation were significantly enriched in Uhrf1-deficient FL-HSCs according to the Gene Ontology (GO) enrichment analysis. We generated gene signatures specific for stemness of HSCs (stem signature) or myeloerythroid progenitors (MEP signature) by subtracting the genes expressed in WT HPC(LK)s from those expressed in WT FL-HSCs or vice versa. Of the stem signature genes, 71.28% showed lower expression and 28.72% showed higher expression in Uhrf1-deficient FL-HSCs compared with WT FL-HSCs. Interestingly, among the MEP signature genes, genes enriched in erythroid differentiation (27.54%) were up-regulated in the absence of Uhrf1, whereas the remaining genes enriched in myeloid-specific genes (72.46%) were suppressed consistent with previous research. Particularly, in comparison to the WT control, Uhrf1-deficient FL-HSCs up-regulated certain erythrocyte differentiation-related genes (e.g., Gata1, Gata2, Gfi1b, Car1, Zfpm1 and Itga2b), most of which were physiologically up-regulated in HPC(LK)s, whereas some genes (Id2, Satb1, Hmga2) that play critical roles in HSC maintenance were down-regulated. These results suggested that Uhrf1 controls the self-renewal versus differentiation of FL-HSCs by suppressing the expression of the erythroid-specific genes and maintaining the expression of HSC stemness genes.

2016-11-30 | GSE85450 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Diabetic db/db Mice Islets Transcriptomes

Project description:Circular RNAs constitute an extensive fraction of the mammalian transcriptome.In this study, circular RNAs dysregulated in the islets of diabetic db/db mice were identified by high-throughput RNA sequencing. More than 5000 circRNAs were detected using RNA sequencing, indicating that circular transcripts were abundant in islets. Among them, we found that circ-Tulp4 showed significant downregulation in diabetic mouse islet cells. Further experiments indicated that modulating the expression of circ-Tulp4 in β cell lines desensitized β-cells to lipotoxicity.

2020-10-28 | GSE138096 | GEO

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