Spatial transcriptomic profiling of livers from mice fed standard or Western diet
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 2000
ORGANISM(S): Mus musculus
SUBMITTER: James Cleland
PROVIDER: E-MTAB-17352 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To test whether sex and diet influence cell-type specific gene expression in the mouse liver, we performed single-nucleus RNA-sequencing on liver tissue from male and female mice fed standard or Western diet.
2026-07-12 | E-MTAB-17281 | biostudies-arrayexpress
Project description:Systemic acute inflammatory signals can cause profound anorexia by disrupting the physiological appetite regulation in the hypothalamic milieu. Conversely, obesity related chronic inflammation of the hypothalamus can disturb anorexigenic signals and promote abnormal body weight control. The aim of the present study was to compare the global hypothalamic endophenotype in C57/Bl6 mice exposed to a high-fat diet or with acute illness mediated by LPS. Ten-week old male C57/Bl6 mice (n=18) were randomly divided into four groups; the control 1 group (n =3) was fed a normal diet whereas the high-fat diet (HFD) group (n =6) was fed a high-fat diet for eight weeks. The control 2 group (n=3) received an intraperitoneal injection of saline whereas the LPS group (n=6) received an intraperitoneal injection of LPS. Mice were sacrificed 18-hr post-injection. Both control 2 and LPS groups were fed a normal diet for eight weeks before the injection. The hypothalamic regions were removed and analysed using a 2D LC-MS methodology. The proteomic analysis profiled 9,235 proteins (q<0.05) across all biological states, of which 522 proteins were found modulated in the HFD group and another 579 in the LPS group. The proteomic profiles demonstrated that the systemic acute inflammation linked with anorexia induced a negative feedback loop of appetite control in the hypothalamus, suggesting an effort to re-establish homeostasis. By contrast, the chronic inflammation associated with obesity initiated a “perpetual cycle” of positive feedback enhancement of appetite regulation further exacerbating positive energy balance.
2018-01-29 | PXD002119 | Pride
Project description:The effects of the administration of maple syrup extract (MSX) on hepatic gene expression were investigated in mice fed high-fat diet. Male C57BL/6J mice aged 3 weeks were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 23 ± 1°C and 49 ± 16% humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). For 1 week acclimation period after purchase, all the mice were fed a low-fat diet (10 kcal% fat). Then, they were randomly divided into three different dietary groups: the first group with the food containing fat at 10 kcal% as low-fat diet, the second group with 45 kcal% as high-fat diet, and the third with HFD plus 0.06% MSX. The mice were fed ad libitum for 8 weeks.
2015-04-30 | E-GEOD-65667 | biostudies-arrayexpress
Project description:During the last few decades, the long-lasting consequences of nutritional programming during the early phase of life have become increasingly evident, but the effects of maternal nutrition on the developing intestine are currently still relatively underexplored. In this study, we investigated in mice the effects of a maternal Western-style (WS) high fat/cholesterol diet, given during the perinatal period, on gene expression and microbiota composition of two-week-old offspring. Microarray analysis revealed that a perinatal WS diet caused significant changes in gene expression in the small intestine and colon of the suckling offspring. A strong sexually dimorphic effect was observed in the affected genes. However, pathway analysis of the differentially expressed genes displayed that in both sexes metabolic and immune functions were strongly affected. Integration of the microbiota and gene expression data applying a multivariate correlation analyses revealed that Bacteroidaceae, Porphyromonadaceae and Lachnospiraceae were the bacterial families that most strongly correlated with gene expression in the colon and not with the bacterial families displaying the most pronounced change due to perinatal exposure to a WS diet. Amongst the genes demonstrating a strong correlation with one or more bacterial families were genes of key importance for intestinal development or functioning (i.e., Pitx2 and Ace2). In conclusion, our data demonstrate a strong programming effect of a maternal WS diet on the development of the intestine in the offspring. Small intestine and colon were isolated from two-week-old pups of dams fed a low- or Western-style high fat/cholesterol diet and subjected to gene expression profiling.
2016-08-22 | E-GEOD-72705 | biostudies-arrayexpress
Project description:This project investigated the molecular mechanism by which *Platycodi Radix* extract (PRE; the ethanol extract of the root of *Platycodon grandiflorum*) prevents non-alcoholic fatty liver disease (NAFLD) in a high-fat diet (HFD)-induced fatty liver mouse model, using a liver-tissue shotgun proteomic and bioinformatic approach. Five-week-old male C57BL/6J mice were acclimatized and then maintained for 12 weeks on one of three diets: a normal chow diet (NCD), a high-fat diet (HFD), or an HFD supplemented with 5% (w/w) PRE. PRE supplementation prevented HFD-induced body-weight gain, fat accumulation, and hepatic steatosis, and improved glucose tolerance and serum lipid profiles. To elucidate the underlying mechanism, liver proteomes of the NCD, HFD, and PRE groups were profiled by LC-MS/MS (n = 3 per group), and proteins differing in relative abundance between NCD vs HFD and HFD vs PRE were interpreted by Ingenuity Pathway Analysis. This LC-MS/MS dataset was designed as a discovery-stage, exploratory screen for hypothesis generation rather than as standalone quantitative proof of differential expression; the resulting candidate proteins and pathways (notably decreased FXR/RXR-activation proteins and increased cholesterol-biosynthesis proteins, predicting enhanced bile-acid synthesis) were subsequently validated by targeted Western blotting and biochemical bile-acid measurement, on which the mechanistic conclusions of the study are based. This dataset comprises the liver-tissue LC-MS/MS data and the protein identification/quantification results supporting the conclusion that PRE prevents hepatic steatosis through modulation of FXR/RXR activation, cholesterol biosynthesis, and bile-acid synthesis pathways.
2026-07-04 | PXD080181 | Pride
Project description:Background: Epidemiological studies suggest an association between maternal obesity and adverse neurodevelopmental outcomes in offspring. Objective: To compare the global proteomic portrait in the cerebral cortex between mice born to mothers on a high-fat or control diet who themselves were fed a high-fat or control diet. Methods: Male mice born to dams fed a control (C) or high fat (H) diet four weeks before conception and during gestation and lactation were assigned to either C or H diet at weaning. Mice (n=24) were sacrificed at 19-weeks and their cerebral cortices were pooled into 8 samples and analysed using an iTRAQ based 2D LC-MS methodology. Results: A total of 6,695 proteins were identified and fully quantified (q<0.01). Approximately 10% of these proteins demonstrated a minimum of one Standard Deviation of regulation across all biological replicates in at least one of the experimental groups (CH, HC, HH) relative to the control (CC). Principal component analysis and hierarchical clustering analysis showed that mice clustered based on the diet of the mother and not their current diet. In silico bioinformatics analysis revealed that maternal high-fat diet was significantly associated with response to hypoxia/oxidative stress and apoptosis in the cerebral cortex of the adult offspring. Conclusion: Maternal high-fat diet was associated with distinct endophenotypic changes of the adult mouse cerebral cortex independent of the diet of the offspring. The identified modulated proteins could represent novel therapeutic targets for the prevention of neuropathological features resulting from maternal obesity.
2018-01-29 | PXD001540 | Pride
Project description:We fed hypercholesterolemic mice high fat diet containing either ticagrelor, clopidogrel, or nothing (control) for 16 weeks, isolated the liver, extracted RNA, and subjected the RNA to RNA-Seq using NGS.
2019-06-16 | E-MTAB-8049 | biostudies-arrayexpress
Project description:The source of most errors in RNA sequencing (RNA-seq) read alignment is in the repetitive structure of the genome and not with the alignment algorithm. Genetic variation away from the reference sequence exacerbates this problem causing reads to be assigned to the wrong location. We developed a method, implemented as the software package Seqnature, to construct the imputed genomes of individuals (individualized genomes) of experimental model organisms including inbred mouse strains and genetically unique outbred animals. Alignment to individualized genomes increases read mapping accuracy and improves transcript abundance estimates. In an application to expression QTL mapping, this approach corrected erroneous linkages and unmasked thousands of hidden associations. Individualized genomes accounting for genetic variation will be useful for human short-read sequencing and other sequencing applications including ChIP-seq. Illumina 100bp single-end liver RNA-seq from 277 male and female Diversity Outbred 26-week old mice raised on standard chow or high fat diet. In addition, Illumina 100bp single-end liver RNA-seq from 128 male 26-week old male mice (20 weeks for NZO strain) from each of the DO founder strains raised on standard chow or high fat diet (8 males per strain by diet group). Each sample was sequenced in 2-4x technical replicates across multiple flowcells. Samples were randomly assigned lanes and multiplexed at 12-24x.
2014-06-10 | E-GEOD-45684 | biostudies-arrayexpress
Project description:We fed hypercholesterolemic mice high fat diet containing either ticagrelor, clopidogrel, or nothing (control) for 16 weeks, isolated the aortae, extracted RNA, and subjected the RNA to RNA-Seq using NGS.
2019-06-16 | E-MTAB-8050 | biostudies-arrayexpress
Project description:Genome-scale analysis of the genetic factors that govern the development of white and brown adipose tissue is still far from complete. In order to identify the key genes that regulate the development of white and brown adipose tissue in mice, the transcriptome analysis was performed on adipose tissues Total RNA obtained from interscapular brown adipose tissue of C57BL/6J mice fed normal diet or high fat diet for 2, 4, 8, 20 and 24 weeks
2015-01-08 | E-GEOD-64718 | biostudies-arrayexpress