ScRNA-seq of pancreatic islets from male and female aged mice with Fltp-reporter sorting
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA872136 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21227976_1.fastq.gz | Fastqsanger.gz | |||
| SRR21227976_2.fastq.gz | Fastqsanger.gz | |||
| SRR21227977_1.fastq.gz | Fastqsanger.gz | |||
| SRR21227977_2.fastq.gz | Fastqsanger.gz | |||
| SRR21227978_1.fastq.gz | Fastqsanger.gz |
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Project description:Single-cell RNA sequencing of pancreatic islets from aged male and female mice. To disect islet heterogeneity we included both sexes and sorted cells based on maturity marker (Fltp).
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Project description:NOD mice deficient in the transcription factor Batf3 never develop diabetes. The goal of this study was to determine if NOD.Batf3-/- mice islets had any inflammatory signature associated with type 1 diabetes. Islets of Langerhans were isolated from NOD, NOD.Batf3-/-, and NOD.Rag1-/- and then compared to determine inflammatory gene profiles. At 6 and 8 weeks of age, NOD.Batf3-/- islets had an absence of inflammatory gene expression and were almost identical to uninflamed NOD.Rag1-/- islets. This work shows that absence of the Batf3 transcription factor is sufficient to prevent all the inflammatory sequelae of autoimmune diabetes. RNA was isolated from the pancreatic islets of Langerhans of 27 experimental mice. Mice were aged either 6 or 8 weeks. Three genotypes were tested: NOD, NOD.Rag1-/-, and NOD.Batf3-/-. There were 3-6 biological replicates per condition. All mice were female. All data was normalized using RMA in Arraystar.
2014-09-29 | E-GEOD-61847 | biostudies-arrayexpress
Project description:Background: Demographic studies have shown that the mean age of patients requiring coronary artery bypass surgery (CABG) is 68 years with approximately 44% of these patients being female . In recent studies, women have been shown to have a significantly greater operative risk as compared to men and that women have worse outcomes after cardiac surgery. Recently we have shown that cardioprotection afforded by cardioplegia is modulated by RNA and protein dependent mechanisms and is significantly decreased with age and in particular is significantly decreased in the aged female. Methods: The mechanisms through which cardioplegia affords cardioprotection are complex and can not be investigated as a single entity but rather must be investigated using a systems approach. To meet these needs we have used microarray and proteomic analysis. The combined use of these two techniques allows for the identification of functionally related gene groups and protein biomarkers. Mature 15 to 20 weeks; 3 to 4 kg) and aged (not senescent, >32 months; 5 to 6 kg) male and female New Zealand White rabbits were used for in situ blood perfused cardiopulmonary bypass. Control hearts received 30 minutes sham ischemia and 120 minutes sham reperfusion. Global ischemia (GI) hearts received 30 minutes of global ischemia. GI was achieved by crossclamping of the aorta. Cardioplegia hearts received cold blood cardioplegia (Deaconess Surgical Associates (DSA) solution (containing 50 uM diazoxide) prior to GI. Following 30 minutes of GI the crossclamp was released, the cardiopulmonary bypass was ceased and the hearts were reperfused for 120 minutes. The hearts were removed flushed of blood and then quick frozen in liquid nitrogen prior to isolation of RNA and protein. Microarray and high throughput proteomic analysis was performed as previously described. Results: Our studies demonstrate that the cardioprotection afforded by cardioplegia is modulated by RNA and protein dependent mechanisms. Our data also show that there are significant differences in the proteins expressed in the mature and aged. Principal component analysis indicated that in the mature male, mature female, and aged male the proteins expressed in control, global ischemia, and cardioplegia were diverse and clustered for individual treatments suggesting that the proteins had different expression levels in each treatment. In contrast, in the aged female the proteins expressed in global ischemia and in cardioplegia were clustered together, suggesting there was no difference in the proteins expressed during global ischemia and with cardioplegia. Glycolysis/gluconeogensis was a significant functional pathway for the aged male but not the mature male or female. Glycolytic and gluconeogenic proteins were significantly up-regulated in the aged male compared to the female and significantly up-regulated in the aged male with cardioplegia as compared to global ischemia. In the aged female 9 unique mitochondrial proteins were up-regulated with cardioplegia. These proteins were associated with oxidative phosphorylation, the electron transport chain, the formation of pyruvate, and the tricarboxylic acid (TCA) cycle, but not glycolysis nor gluconeogenesis. Conclusions: Our study demonstrates that the mitochondrion plays a key role in age and gender specific cardioprotection. The identification of these specific pathways and biomarkers should allow for the development of age and gender specific cardioprotection and significantly decrease morbidity and mortality in the aged female. Rabbit heart (atria and ventricles):control vs. global ischemia; control vs. cardioplegia; cardioplegia vs. global ischemia
2011-06-28 | E-GEOD-30261 | biostudies-arrayexpress
Project description:Objective: SORCS2 is an intracellular sorting receptor genetically associated with body mass index (BMI) in humans, yet its mode of action remains unknown. Elucidating the receptor function that defines its role in metabolic health is the objective of this work. Methods: Combining in vivo metabolic studies in SORCS2-deficient mouse models with ex vivo structural and functional analyses as well as single-cell transcriptomics of murine pancreatic tissues, we studied the pathophysiological consequences of receptor dysfunction for metabolism. Results: Our studies identified an important role for SORCS2 in islet stress response essential to sustain glucose-stimulated insulin release. In detail, we show that SORCS2 is predominantly expressed in islet alpha cells. Loss of expression impairs the ability of these cells to produce osteopontin, a secreted factor that facilitates insulin release from beta cells under stress. In line with diminished osteopontin levels, beta cells in SORCS2-deficient islets show changes in gene expression related to aggravated stress, protein misfolding, as well as mitochondrial dysfunction; and they exhibit defects in insulin granule maturation and a blunted response to glucose stimulation in vivo and ex vivo. Impaired glucose tolerance in receptor mutant mice coincides with alterations in body weight and composition. Conclusion: Our data identified a novel concept in protective islet stress response involving the alpha cell receptor SORCS2, and they provide experimental support for association of SORCS2 with metabolic control in humans.
2023-05-10 | GSE231551 | GEO
Project description:Background: Demographic studies have shown that the mean age of patients requiring coronary artery bypass surgery (CABG) is 68 years with approximately 44% of these patients being female . In recent studies, women have been shown to have a significantly greater operative risk as compared to men and that women have worse outcomes after cardiac surgery. Recently we have shown that cardioprotection afforded by cardioplegia is modulated by RNA and protein dependent mechanisms and is significantly decreased with age and in particular is significantly decreased in the aged female. Methods: The mechanisms through which cardioplegia affords cardioprotection are complex and can not be investigated as a single entity but rather must be investigated using a systems approach. To meet these needs we have used microarray and proteomic analysis. The combined use of these two techniques allows for the identification of functionally related gene groups and protein biomarkers. Mature 15 to 20 weeks; 3 to 4 kg) and aged (not senescent, >32 months; 5 to 6 kg) male and female New Zealand White rabbits were used for in situ blood perfused cardiopulmonary bypass. Control hearts received 30 minutes sham ischemia and 120 minutes sham reperfusion. Global ischemia (GI) hearts received 30 minutes of global ischemia. GI was achieved by crossclamping of the aorta. Cardioplegia hearts received cold blood cardioplegia (Deaconess Surgical Associates (DSA) solution (containing 50 uM diazoxide) prior to GI. Following 30 minutes of GI the crossclamp was released, the cardiopulmonary bypass was ceased and the hearts were reperfused for 120 minutes. The hearts were removed flushed of blood and then quick frozen in liquid nitrogen prior to isolation of RNA and protein. Microarray and high throughput proteomic analysis was performed as previously described. Results: Our studies demonstrate that the cardioprotection afforded by cardioplegia is modulated by RNA and protein dependent mechanisms. Our data also show that there are significant differences in the proteins expressed in the mature and aged. Principal component analysis indicated that in the mature male, mature female, and aged male the proteins expressed in control, global ischemia, and cardioplegia were diverse and clustered for individual treatments suggesting that the proteins had different expression levels in each treatment. In contrast, in the aged female the proteins expressed in global ischemia and in cardioplegia were clustered together, suggesting there was no difference in the proteins expressed during global ischemia and with cardioplegia. Glycolysis/gluconeogensis was a significant functional pathway for the aged male but not the mature male or female. Glycolytic and gluconeogenic proteins were significantly up-regulated in the aged male compared to the female and significantly up-regulated in the aged male with cardioplegia as compared to global ischemia. In the aged female 9 unique mitochondrial proteins were up-regulated with cardioplegia. These proteins were associated with oxidative phosphorylation, the electron transport chain, the formation of pyruvate, and the tricarboxylic acid (TCA) cycle, but not glycolysis nor gluconeogenesis. Conclusions: Our study demonstrates that the mitochondrion plays a key role in age and gender specific cardioprotection. The identification of these specific pathways and biomarkers should allow for the development of age and gender specific cardioprotection and significantly decrease morbidity and mortality in the aged female.
2011-06-28 | GSE30261 | GEO
Project description:M-NM-2-cell identity is determined by tightly regulated transcriptional networks that are modulated by extracellular cues, thereby ensuring M-NM-2-cell adaptation to the organismM-bM-^@M-^Ys insulin demands. We have observed in pancreatic islets that stimulatory glucose concentrations induced a gene profile that was similar to that of freshly isolated islets, indicating that glucose-elicited cues are involved in maintaining M-NM-2-cell identity. Low glucose induces the expression of ubiquitous genes involved in stress responses, nutrient sensing, and organelle biogenesis. By contrast, stimulatory glucose concentrations activate genes with a more restricted expression pattern (M-NM-2- and neuronal- cell identity). Consistently, glucose-induced genes are globally reduced in islets deficient with Hnf1a (MODY3), characterized by a deficient glucose metabolism. Of interest, a cell cycle gene module was the most enriched among the variable genes between intermediate and stimulatory glucose concentrations. Glucose regulation of the islet transcriptome was unexpectedly broadly maintained in islets from aged mice. However, the cell cycle gene module is selectively lost in old islets and the glucose activation of this module is not recovered even in the absence of the cell cycle inhibitor p16. We used microarrays to detail the global programme of gene expression regulated by glucose in young and aged pancreatic islets as well as freshly-isolated islets. Pancreatic islets from young and old mice were isolated and cultured at different glucose concentrations for RNA extraction and hybridization on Affymetrix microarrays. Islets were cultured at 3mM (G3), 5.5mM (G5), 11mM (G11) and 16mM (G16). Freshly-isolated islets (F) were also processed for RNA extraction . We also assessed the dynamic glucose regulation of gene expression at different time-points after an overnight at 3mM (T0): after 1h at 11mM (T1) and after 4h (T4).
2013-07-01 | E-GEOD-42591 | biostudies-arrayexpress