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

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

PROVIDER: PRJNA587103 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10384569_1.fastq.gz	Fastqsanger.gz
	SRR10384569_2.fastq.gz	Fastqsanger.gz
	SRR10384570_1.fastq.gz	Fastqsanger.gz
	SRR10384570_2.fastq.gz	Fastqsanger.gz
	SRR10384571_1.fastq.gz	Fastqsanger.gz

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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 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.

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

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

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Study of the tRNA-derived fragment expression profile in mouse pancreatic islets of pre-diabetic obese db/db mice

Project description:In this study, we discovered cytosolic and mitochondrial fragments resulting from tRNA and mt-tRNA cleavage, which may act as new regulators of cellular and metabolic functions. We analyzed hundreds of these fragments in the pancreatic islets of db/db mice and compared them to heterozygous control db/+ mice. At 16 weeks of age, db/db mice exhibit obesity, insulin resistance, and glucose intolerance. In our analysis, we identified 3858 tRFs in the islets of db/db mice, among which 342 exhibited significant changes (≥ 2 fold; adjusted p value ≤ 0.05) compared to controls. Of these, 199 tRFs showed increased levels, while 170 tRFs showed decreased levels in the pre-diabetic mice. Notably, a striking majority (147 out of 170) of the tRFs with reduced abundance in the islets of db/db mice were derived from the cleavage of tRNAs encoded by the mitochondrial genome. Our findings reveal a significant reshaping of mitochondrial tRFs in pre-diabetic conditions, coinciding with a well-established mitochondrial metabolic defect under these conditions. Specifically, we demonstrated that a fragment (named mt-tRF-LeuTAA) resulting from the cleavage of mt-tRNA-LeuTAA, encoded by the mitochondrial genome and found to be reduced in the islets of db/db mice, acts as a key regulator of mitochondrial OXPHOS functions, mitochondrial membrane potential, the insulin secretory capacity of ß-cells, and the insulin sensitivity of myotube muscle cells.

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Expression analysis in pancreatic and liver tissues of diabetic db/db mice in response to dietary supplementation with selenate

Project description:Investigation of gene expression level changes in pancreatic and liver tissues of diabetic db/db mice supplemented with selenate, compared to the diabetic db/db mice administered placebo. Fasting blood glucose levels increased continuously in diabetic db/db mice administered placebo (DMCtrl) but decreased gradually in selenate-supplemented diabetic db/db mice (DMSe) and approached normal values when the experiment ended. The size of pancreatic islets increased, causing the plasma insulin concentration to double in DMSe mice compared with that in DMCtrl mice. Two six chip studies using total RNA respectively isolated from pancreatic and liver tissues of three selenate-supplemented diabetic db/db mice, and three diabetic db/db mice administered placebo.

2014-03-07 | E-GEOD-55636 | biostudies-arrayexpress

Expression analysis in pancreatic and liver tissues of diabetic db/db mice in response to dietary supplementation with selenate

2014-03-07 | GSE55636 | GEO

Profiling pancreatic islets from obese db/db and lean control db/+ mice

Project description:This program addresses the molecular basis of beta-cell failure associated with the development of type 2 diabetes in the db/db mice. Specifically, which genes are differentially expressed in pancreatic islets of the db/db mice compared to the control db/+ mice? The db/db mice islets profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the islets of db/db mice compared to the corresponding db/+ controls.

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Project description:Purpose: RNA seq analysis were to compare and contrast the gene expression profile involved in the dedifferentiation of db/db islets in type 2 diabetes Methods: Islets of wild type, db/+ and db/db were purified using perfusion from 12 week old mice and RNA were isolated. Islated RNA were used in RNA seq to understand the expression pattern Results: Using an optimized data analysis workflow, we mapped about 10 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts WT, db/+ and db/db mice islets with TopHat workflow. Hierarchical clustering of differentially expressed genes uncovered there role in type 2 diabetes. Data analysis with TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: We characterised and identified genes involved in dedifferentiation of islets.

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Project description:diabetes, mouse models, diabetic nephropathy, streptozotocin db/db Keywords: other

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Profiling pancreatic islets from obese db/db and lean control db/+ mice

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