Liver Transcriptomics from Male and Female Mice of Three Strains on Control, Medium Protein and Low Protein Diets
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PROVIDER: PRJNA751536 | ENA |
REPOSITORIES: ENA
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Project description:Mice were put on either a control, medium or low protein diet and their liver transcriptomic expression was measured after 13 weeks on diet after an overnight fast. This was to discover the impact of sex, strain and protein level on the metabolism of the liver.
2021-11-18 | GSE181301 | GEO
Project description:The ratio of energy to protein in the finishing diet of growing pigs can impact on IMF content with consequences for pork quality. The objective of this study was to compare gene expression profiles of Musculus semimembranosus (SM) of animals divergent for IMF as a consequence of protein dietary restriction in an isocaloric diet. The animal model was derived through the imposition of low or high protein diets during the finisher stage in Duroc gilts. RNA was extracted from post mortem SM tissue, processed and hybridised to Affymetrix porcine GeneChip® arrays. Eleven purebred Duroc gilts were blocked on the basis of initial body weight and assigned to one of two dietary treatments. High (HP) and low protein (LP) diets were formulated to contain 217 and 128 g/kg crude protein (CP) respectively. The HP and LP diets contained 13.0 and 7 g/kg of total lysine, respectively. Downward adjustment of CP was achieved by increasing the wheat:soyabean meal ratio. Diets were isocaloric, formulated to an estimated digestible energy (DE) density of 14 MJ/kg.
2014-01-31 | E-GEOD-44326 | biostudies-arrayexpress
Project description:Calorie restriction (CR) increases lifespan and improves brain health in mice. Ad libitum low protein, high carbohydrate (LPHC) diets also extend lifespan, but it is not known whether they are beneficial for brain health. We compared hippocampus biology and memory in mice subjected to 20% CR or provided ad libitum access to one of three LPHC diets, or to a control diet. At age 15 months, patterns of RNA expression in the hippocampus were similar between CR and LPHC diets for genes associated with longevity, cytokines and dendrite morphogenesis. Nutrient sensing proteins including SIRT1, mTOR and PGC1α were also influenced by diet, however the effects varied by sex. CR and LPHC diets were associated with increased dendritic spines in dentate gyrus neurons. CR and LPHC diets led to modest improvements in the Barnes Maze and Novel Object Recognition. LPHC diets recapitulate some of the benefits of CR on brain aging.
2018-10-18 | GSE111778 | GEO
Project description:The ratio of energy to protein in the finishing diet of growing pigs can impact on IMF content with consequences for pork quality. The objective of this study was to compare gene expression profiles of Musculus semimembranosus (SM) of animals divergent for IMF as a consequence of protein dietary restriction in an isocaloric diet. The animal model was derived through the imposition of low or high protein diets during the finisher stage in Duroc gilts. RNA was extracted from post mortem SM tissue, processed and hybridised to Affymetrix porcine GeneChip® arrays.
2014-01-31 | GSE44326 | GEO
Project description:Early life nutritional imbalances are risk factors for metabolic dysfunctions in adulthood, but the effects of perinatal exposure to high versus low protein diets are poorly understood. We exposed C57BL/6 offspring to a high protein/low carbohydrate (HP/LC) or low protein/high carbohydrate (LP/HC) diet during gestation and lactation, and measured metabolic phenotypes between birth and ten months of age in male offspring. Perinatal HP/LC and LP/HC exposures resulted in a decreased ability to clear glucose in the offspring, with reduced baseline insulin and glucose levels in the LP/HC group and a reduced insulin response post-glucose challenge in the HP/LC group. The LP/HC diet group also showed reduced weight at birth and at weaning age, whereas the HP/LC offspring showed an increased weight at weaning and increased adiposity after 5 months of age. Gene expression profiling of hypothalamic and liver tissues indicated alterations of diverse molecular pathways by both diets. Specifically, hypothalamic transcriptome and pathway analyses indicate perturbations of MAPK and hedgehog signaling, processes associated with neural restructuring and transmission, and phosphate metabolism by perinatal protein imbalances. Liver transcriptome data revealed changes in purine and phosphate metabolism, hedgehog signaling, and circadian rhythm pathways. Our results support that maternal protein imbalances perturb molecular pathways in central and peripheral metabolic tissues and predispose offspring to metabolic dysfunctions.
2018-10-01 | GSE120548 | GEO
Project description:Purpose: To investigate graded levels of low protien dites effects on hypothalamic gene expression pattern, RNA-seq was performed on hypothalamus of mice treated with different levels of low protein and normal protein under both 60% fat and 20% fat conditions. Methods: There were 8 diets in total, the fat content of first 4 diets were fixed at 60% fat level by energy and protein was varied from 1% to 20% (1%, 2.5%, 5% and 20% respectively) by energy (D14121903, D14121904, D14071601,D14071604), another 4 kinds of diets contained the same graded levels of protein content as the first 4 diets but fat contents were fixed at 20% by energy (D14121905, D14121906, D14071607, D14071610). The remaining energy was compensated of carbohydrate which included corn starch and maltodextrose. Casein was used as the protein source in all diets. To mimic the typical western diet a mix of cocoa butter, menhaden oil, sunflower oil, palm oil and coconut oil was used as the fat source and was designed to generate a 47.5: 36.8: 15.8 proportion of saturated, mono-unsaturated and polyunsaturated fats and 14.7: 1 proportion of n-6 and n-3 fatty acids, the proportions of different fat compositions didn’t change under two different 60% and 20% fat conditions. Sucrose and cellulose were fixed at 5% level by energy and standard vitamin and mineral mix were also added to all diets as well (Hu et al., 2018). The two series were isocaloric within each series. Diets can be ordered direct from research diets (https://researchdiets.com) using the diet codes provided. The hypothalamus of 6 individuals were collected for each diet group, 3 of which were pooled together as one sample, resulting in each group having 2 pooled samples of 3 hypothalamus. Hypothalamic RNA was extracted using Trizol method described in star methods in paper and then sent to Beijing Genomic Institute (BGI) for RNA sequencing. All RNA sequencing was measured by using the BGI-seq 500 sequencer. To determine the sequencing quality of each sample, FASTQ raw data files were measured by using fastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) quality control tool, after confirmed sequencing quality of each sample, raw reads were aligned to the Mus musculus reference genome (GRCm38) using HISAT2-2.1.0 (Kim et al., 2015; Pertea et al., 2016) and Samtools-1.2 modules (Li et al., 2009), and then featureCounts (Liao et al., 2014) tool in Subread-5.0 (Liao et al., 2013) was used to get counts for each sample from BAM files which was obtained from alignment step. To exclude the low counts, only genes with counts per million (CPM) value > 1 were included in the further analysis. Counts were normalized by the trimmed means of M values (TMM normalization) (Robinson and Oshlack, 2010) method in the edgeR (Anders et al., 2013; Lund et al., 2012; McCarthy et al., 2012; Robinson et al., 2010; Robinson and Oshlack, 2010; Robinson and Smyth, 2007) package. To investigate different dietary protein contents under fixed two levels fat content effects on gene expression levels Generalized Linear Modelling (GLM) function in R-3.5.3 edgeR package was used, The GLM model used in this study were: ~P+F+P:F, which means regression against protein (P) and fat contents (F) of diets plus their interaction (P:F). If the interaction effect was not significant (p > 0.05), the interaction was not included in the analysis and a revised model (~P+F) was utilized (Hu et al., 2018). To explore significantly correlated genes with dietary protein content respectively under 60% fat and 20% fat conditions, Pearson correlation analysis was performed for normalized log counts of all genes by using Pearson correlation method in R-3.5.3. Then selected the significantly correlated genes with dietary protein content (GLM: p < 0.05) respectively in the GLM and Pearson correlation (Pearson: p < 0.05 for 60% fat and 20% fat conditions) analysis were loaded into the Ingenuity pathway analysis (IPA) program (Ingenuity Systems; http://www.ingenuity.com/) to observe the significantly affected pathways. Results: The most affected pathways by the dietary low protein included the mTOR signaling pathway, the hunger signaling pathway, eIF2a signaling pathway and regulation of eIF4 and p70S6K signaling pathway. In the hunger signal pathway, we found there were strong correlations for four key hunger signaling pathway genes Pomc, Cart, Npy and Agrp with the protein content in the diet across different protein content groups (from 1% protein to 20% protein group) with Pomc and Cart expression significantly reduced as protein level declined while Npy and Agrp expression increased as protein levels decreased.
2021-03-04 | GSE158215 | GEO
Project description:Inadequate dietary protein intake causes adverse changes in the morphology and function of skeletal muscle. These changes may be reflected in early alterations in muscle mRNA levels. Microarray analysis was used to assess whether inadequate protein intake differentially affects skeletal muscle transcript levels and expression profiles in older adults. Experiment Overall Design: 11 older males and females (aged 55-80 y) consumed controlled diets that contained 1.2 g proteinâ¢kg-1â¢d-1 (adequate protein) for one wk and then 0.5 g proteinâ¢kg-1â¢d-1 (inadequate protein; IP group; n=11) for a second wk. RNA was isolated from fasting-state vastus lateralis biopsies obtained at the end of each period and the transcript levels were determined using the Affymetrix U133A array
2008-06-16 | E-GEOD-8441 | biostudies-arrayexpress
Project description:We utilized three ecologically diverse Drosophila species to explore the influence of ecological adaptation on transcriptomic responses to isocaloric diets differing in their relative proportions of protein to sugar. Drosophila melanogaster, a cosmopolitan species that breeds in decaying fruit, exemplifies individuals long exposed to a Western diet higher in sugar, while the natural diet of the cactophilic D. mojavensis, is much lower in carbohydrates. Drosophila arizonae, the sister species of D. mojavensis, is largely cactophilic, but also utilizes rotting fruits that are higher in sugars than cacti. We exposed third instar larvae for 24 hours to diets either (1) high in protein relative to sugar, (2) diets with equal amounts of protein and sugar, and (3) diets low in protein but high in sugar. As we predicted, based upon earlier interspecific studies of development and metabolism, the most extreme differences in gene expression under different dietary conditions were found in D. mojavensis followed by D. arizonae. No differential expression among diets was observed for D. melanogaster, a species that survives well under all three conditions, with little impact on its metabolism. We suggest that these three species together provide a model to examine individual and population differences in vulnerability to lifestyle-associated health problems such as metabolic syndrome and diabetes.
2017-07-20 | GSE101664 | GEO
Project description:Maternal high-protein and low-protein diets perturb hypothalamus and liver transcriptome and metabolic homeostasis in adult mouse offspring
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Project description:Effect of extreme protein low diets of PKU and UCD patients on the gut microbiota
| PRJEB41032 | ENA