Direct RNA sequencing experiment of major tissues from wild-type mice under fasting and fed treatments
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE267281 | GEO | 2025/02/12
REPOSITORIES: GEO
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Project description:Male C57BL/6 mice, sourced from the Jackson Laboratory, were acquired at 12 weeks of age. The mice were housed in groups of three per cage, with unrestricted access to water and a standard chow diet. For the experimental treatments involving fasting and fed states (n = 3 per group), the mice were either provided continuous access to food or subjected to a 24-hour fasting period before euthanasia at 10 am for tissue collection.
2025-02-12 | GSE267280 | GEO
Project description:Male C57BL/6 mice, sourced from the Jackson Laboratory, were acquired at 12 weeks of age. The mice were housed in groups of three per cage, with unrestricted access to water and a standard chow diet. For the experimental treatments involving fasting and fed states (n = 3 per group), the mice were either provided continuous access to food or subjected to a 24-hour fasting period before euthanasia at 10 am for tissue collection. The tissues harvested included muscle, liver, heart, lungs, both white and brown adipose tissues, spleen, and kidney. These tissues were immediately preserved in liquid nitrogen post-sacrifice to maintain their integrity for subsequent analyses.
2025-02-12 | GSE267279 | GEO
Project description:Mammalian energy homeostasis is regulated by the hypothalamus and hindbrain, with the hippocampus, midbrain nuclei, and other regions implicated by evidence from human genetics studies. In order to understand how these brain regions respond to imbalances in energy homeostasis, we performed two experiments examining the effects of different diets in male C57BL6 mice. In our first study, groups of 6 pair-housed mice were given access to chow, high-fat diet or fasted for 16 hours. In our subsequent study, two groups of 10 mice were single-housed and given access to chow or fasted for 24h. We recorded food intake for each cage, the change in body weight for each animal, and collected hypothalamus, hippocampus, superior colliculus, inferior colliculus, prefrontal cortex, and zona incerta samples. We performed bulk RNA sequencing on 185 samples and validated them by a series of quality control assessments including alignment quality and gene expression profiling. We believe these studies capture the transcriptomic effects of acute fasting and high fat diet in the rodent brain and provide a valuable reference.
2023-11-21 | GSE236077 | GEO
Project description:Gastric ECL cells and parietal (PC) cells in normal conditions and gastric ECL cells after 24 hrs fasting were purified using a combination of counter-flow elutriation, nycodenz gradient and FACS based on acridine orange labeling of histamine containing vesicles (ECL cells) or autofluorescense (PC cells) to homogeneity. cRNA probes from this purified cell suspensions and from mixed gastric homogenates were hybridized to whole rat genome expression oligonucleotide microarrays. We imported each channel separately (normalized intensity of Cy3 labeled samples = gProcessedSignal and of Cy5 labeled samples = rProcessedSignal) from the original Agilent Feature Extraction data files (submitted as raw data) after slide scanning from all slides into a Genespring 7.3 microarray database warehouse. Genespringâs built in statistical module was used to compare all channels to each other. The normalization used was against specific samples (the 5 channels of Gastric mucosal scrapings). Genespring identifies genes differentially expressed in the ECL cell samples and the parietal samples and also calculates the significance of difference (p-value). Experiment Overall Design: ECL cells: free access to food and water (250 gm Sprague Dawley Rat) Experiment Overall Design: PC cells: free access to food and water (250 gm Sprague Dawley Rat) Experiment Overall Design: ECL cells: 24 hrs fasting, free access to water (250 gm Sprague Dawley Rat) Experiment Overall Design: Gastric mucosa scrapes: free access to food and water (250 gm Sprague Dawley Rat) Experiment Overall Design: Fasting gastric mucosa scrapes: 24 hrs fasting, free access to water (250 gm Sprague Dawley Rat) Experiment Overall Design: Three independent cell purifications, total RNA isolations and at least one dye swap per sample set (3).
2008-06-14 | E-GEOD-6204 | biostudies-arrayexpress
Project description:Temporally restricted feeding has a profound effect on the circadian clock. Fasting and feeding paradigms are known to influence hepatic transcription. This dataset shows the dynamic effects of refeeding mice after a 24hour fasting period. Mice were entrained for two weeks under ad libitum access to food. Mice were then released into constant darkness and food was withdrawn at CT4 on the first day in constant darkness. On the second day in constant darkness mice were either fed (Refed) or continously fasted (Fast) at CT4. Liver tissue was collected at the indicated timepoints. Total RNA was extracted and standard Affymetrix protocol were used for amplification, labeling and hybridization
2009-11-23 | E-GEOD-13063 | biostudies-arrayexpress
Project description:We reported a 16-week intermittent fasting intervention alleviated cognitive impairment in Alzheimer's disease. Here we present transcriptomics data of mice hippocampus to further investigate how intermittent fasting regulates vital biological processes and pathways. After mapping clean RNA-seq reads of all mice against the Mus musculus genome, we detected 56,412 genes (including 12,527 new predicted genes) with fragments per kilobase of transcripts per million mapped reads (FPKM) value. Gene set enrichment analysis (GSEA) was used for pathway or functional analysis of RNA-seq data.
2021-12-31 | GSE164461 | GEO
Project description:Background; In the postabsorptive state, the portal-drained viscera are a major energy consumer, but a comprehensive overview of the adaptive fasting response in the liver is lacking. Hence, gene-expression profiling, pathway, network and gene-set enrichment analysis and immunohistochemistry were carried out on mouse liver after 0, 12, 24, and 72 hours of fasting. Results; Liver weight has fallen to 50% of control after three days of fasting, hepatocyte size was reduced with no apparent increase in apoptosis, while the basic liver structure and metabolic zonnation were preserved. Expression profiling and pathway analysis depicted four master processes, all with response peaking at 24 hours, and all but one decreasing towards 72h. Changes in gene expression were compatible with cellular energy deficiency, and metabolic adaptations were directed at enhanced glucose production, stimulation of lipid catabolism and ketone body synthesis, and strongly augmented ATP production. Consequently, the expression of genes involved in oxidative and endoplasmic reticulum stress response was increased. In addition, urea cycle genes were strongly upregulated during whole duration of fasting, in spite no obvious increase in amino-acid catabolism. Major physiological change upon continued fasting was restoration of glycogen reserves, but with reverse localization, demonstrating utilization of different glycogenic precursor compared to the fed controls. Conclusion; The changes in liver gene expression indicate a rapid onset of generating glucose and ketone bodies during short, and a return to near normal situation in prolonged fasting. The reason apparently lies in glycogen repletion, due to late fasting glucose production by (gut and) kidney. Experiment Overall Design: Male FVB mice (Charles River, Maastricht, The Netherlands) were housed at 20-22°C, 50-60% humidity, a 12 hours light/dark cycle, and food and water ad libitum. At 6 weeks of age, mice were fasted by removing chow for up to 72 hours before sacrifice (n = 6 per group). All animals were sacrificed between 9:00 and 10:00 a.m. by cervical dislocation. The liver was removed quickly, weighed, snap-frozen in liquid N2, and stored at -80°C. Total intestinal RNA was extracted from frozen tissue using TRIzol (Invitrogen), followed by a cleanup through a RNeasy column (Qiagen). The quality of RNA was assessed with the RNA 6000 Nano LabChip® Kit in an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA). The 60-mer Mouse Development (22K) Oligo Microarray G4120A (Agilent) was used. Three arrays per experimental condition were used. Per microarray, 20 μg mRNA, pooled from 2 livers, was reverse transcribed with Cy3-labelled dCTP (Perkin Elmer, Boston, USA), using the Agilent Fluorescent Direct Label Kit. Cy5-labeled cDNA produced from RNA pooled from livers of 6 fed animals served as the common reference across all arrays. Hybridized cDNAs were detected with Agilentâ??s dual-laser microarray slide scanner. The data were retrieved with Agilentâ??s Feature Extraction software 6.1.1.
2008-11-21 | E-GEOD-10653 | biostudies-arrayexpress
Project description:The effects of fasting have been studied extensively, predominantly on isolated processes, within a specific organ. No comprehensive study of the adaptations was available for different organs, let alone interrelating them, which left the understanding of the body’s orchestration of fasting response limited. The gene expression profiles of brain, small intestine, kidney, liver and skeletal muscle were therefore studied in mice subjected to short, moderate and prolonged fasting. Functional category enrichment, network, and text-mining analyses were employed to scrutinize the overall adaptive response, aiming to identify responsive pathways, processes and networks, and their regulation. The implicated processes did not follow the accepted carbohydrate-lipid-protein succession of energy substrates expenditure. Instead, they were activated simultaneously in different organs during the whole duration of fasting. The most prominent changes occurred in lipid and steroid metabolism, especially in the liver and kidney, which showed biochemically similar, orchestrated responses. They were accompanied by suppression of the immune response and cell turnover, particularly in the small intestine, tied in with increased proteolysis in the muscle. Enhanced defence against oxidative damage, obvious in all the organs, was the top reaction of the brain, otherwise shown to be extremely well protected from starvation. The major transcription regulators of fasting response in different organs were FoxO transcription factors, AP-1, p53, cMyc, Sp1, EGF and HNF4α. The revealed interorgan interactions between metabolic, inflammatory and cell turnover responses are essential when designing strategies to treat the starvation affected individuals, while stressing the significance of using complimentary bioinformatics tools in the high-throughput data analysis. 6 week-old male FVB mice were fasted for 0, 12, 24, 48 or 72 hours before sacrifice (N = 5 per group). From each mouse total RNA was isolated from five organs - liver, small intestine, kidney, brain, and calf muscle. Five microarrays per experimental condition (five tissues, five timepoints) were performed. We used a common reference design. The single common-reference sample was a pool of equal amounts of RNA from all the samples investigated, including additional samples from 5 mice that were fasted for 48 hours and supplemented with vitamin B complex after 24 and 36 hours of fasting.
2011-03-09 | E-GEOD-24504 | biostudies-arrayexpress
Project description:Analysis of fasting-induced change of metabolites in mice confirmed that glucose level was reduced in the liver, but unaffected in the brain of fasted mice. To explore molecular mechanisms for the preferential glucose supply to the brain upon fasting, we compared gene expression profiles of the brain between fasted and fed mice. Gene ontology (GO) term analysis revealed the enrichment of one GO term, “active membrane transporters activity”. We also showed that fasting enhances the expression of a glucose transporter Slc2a1 (Glut1) gene.
2015-11-14 | GSE72987 | GEO
Project description:Short-term fasting elicits beneficial effects in mice and humans, including protection from chemotherapy toxicity, but the involved mechanisms are not well understood. We collected blood samples from healthy human volunteers and mice before and after 36 or 24 hours of fasting, respectively, to measure fatty acid composition of erythrocyte membranes, circulating miRNAs, and RNA expression at PBMCs. In both mice and humans, fasting affected the proportion of polyunsaturated versus saturated and monounsaturated fatty acids at the erythrocyte membrane. Also, fasting significantly reduced the expression at PBMCs of insulin signaling-related genes, including the SREBP lipid-metabolizing pathway, in correlation with changes in membrane fatty acids. We tested the relevance of these fatty acid homeostasis parameters using a complete platform to monitor chemotherapy toxicity in mice. When fasted for 24 hours before and 24 hours after administration of the chemotherapeutic drug oxaliplatin, mice showed a strong protection from kidney, liver, heart and bone marrow toxicity. Importantly, the newly discovered fasting parameters defined two clearly separated groups of individuals that accurately predicted a differential protection from chemotherapy toxicity. Our results reveal a novel mechanism of fasting associated with fatty acids homeostasis, and provide novel biomarkers of fasting to predict fasting-mediated protection from chemotherapy toxicity.
2022-06-12 | GSE173241 | GEO