Liver transcriptome comparison of divergently selected Lean and Fat mouse lines in cholesterol homeostasis, bile acids, glucose and lipoprotein metabolism
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE24967 | GEO | 2011/10/17
SECONDARY ACCESSION(S): PRJNA131893
REPOSITORIES: GEO
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Project description:This study aimed to identify molecular basis of obesity-resistant mechanisms in the Lean line with the emphasis on lipid homeostasis. Expression profiling using custom Steroltalk v2 microarray demonstrated that Lean mice exhibit a higher hepatic expression of cholesterol synthesis genes compared to the Fat line. A significant difference between the strains was also found in the bile acid metabolism. We identified novel candidate molecular targets by which we can at least in part explain resistance to obesity development in the Lean line. Direct comparison of 10 Lean and 10 Fat mouse samples. For 7 out of 10 comparisons dye-swap technical replication were performed.
2011-10-16 | E-GEOD-24967 | biostudies-arrayexpress
Project description:The lean and fat broilers were derived from the 21st generation of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). In brief, broilers in the two lines (lean line and fat line) of the NEAUHLF have the same Arbor Acres ancestry, but were divergently selected by the concentration of very low-density lipoprotein and abdominal fat percentage (AFP) at 7 weeks old. After 21 generations of selection, there is over a 10-fold difference in abdominal fat percentage between the two lines, representing a classical obese-lean-study model. At age of 7 weeks, ten male individuals of each line were selected randomly to investigate the interactions between gut microbiome, host gene expression and obesity.
2022-02-02 | GSE179459 | GEO
Project description:Obtaining adipose tissue samples are paramount to the understanding of human obesity. We have examined the impact of needle-aspirated and surgical biopsy techniques on the study of subcutaneous adipose tissue (scAT) gene expression in both obese and lean subjects. Biopsy sampling methods have a significant impact on data interpretation and revealed that gene expression profiles derived from surgical tissue biopsies better capture the significant changes in molecular pathways associated with obesity. We hypothesize that this is because needle biopsies do not aspirate the fibrotic fraction of scAT; which subsequently results in an under-representation of the inflammatory and metabolic changes that coincide with obesity. This analysis revealed that the biopsy technique influences the gene expression underlying the biological themes commonly discussed in obesity (e.g. inflammation, extracellular matrix, metabolism, etc), and is therefore a caveat to consider when designing microarray experiments. These results have crucial implications for the clinical and physiopathological understanding of human obesity and therapeutic approaches. Keywords: subject and tissue biopsy technique comparison Tissue samples from lean and obese subjects were analyzed: total of 36 hybridizations. The goal was to compare the effect of biopsy sampling methods on global subcutaneous adipose tissue gene expression analyses. The following subject groups were used for the analysis: 9 lean subjects: needle biopsy 9 lean subjects: surgical biopsy 9 obese subjects: needle biopsy 9 obese subjects: surgical biopsy
2008-12-22 | E-GEOD-12050 | biostudies-arrayexpress
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile hepatic gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in liver during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with a two-stage mixed model. A total of 905 differentially expressed "functional" genes were identified (FDR<0.10). The greatest number of differentially expressed genes (400) was detected at 7 weeks of age. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes
2007-09-01 | GSE8812 | GEO
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile pituitary gland gene expression during juvenile development (1 to 7 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia, and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in the pituitary gland during juvenile development using a reference design for the hybridization of total RNA from the pituitary gland. A reference RNA pool was made from an equal amount of high-quality total RNA extracted from all of the samples. Each of the microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the pituitary samples and Cy5-labled cDNA targets from the reference pituitary RNA pool. Log2-transformed fluorescence intensities were analyzed with a mixed model. Two-way ANOVA (SAS) of log2 ratios was used to detect significant (p<0.05) differences by line, age, and the line-by-age interaction. There were 1150 significantly different genes between the two lines, and 339 of these genes exhibited greater than 0.68-fold differences in their log2 ratios (highest group mean at least 160% of the lowest group mean). One thousand four hundred twenty nine genes were significantly different by age and of these, 583 exhibited fold changes greater than 0.68 in the log2 ratio. There were 145 genes that significantly differed in their line-by-age interaction, and 62 of these exhibited greater than 0.68-fold differences. There were 386 genes with significant differences by line or for line-by-age interaction with at least a 0.68-fold change in log2 ratio and n ≥ 2 for each experimental group. Four biological replicates were analyzed, each consisting of a complete set of individual samples from pituitary glands of Fat and Lean line chickens at week 1, week 3, week 5, or week 7 of age. Amplified antisense RNA from each sample was analyzed using Del-Mar 14 K array in a reference design. Each experimental sample (Fat and Lean Weeks 1, 3, 5, and 7) was labeled with Cy3 and hybridized with an aliquot of the Cy5 reference pool, which was generated from all 32 RNA samples.
2011-01-13 | E-GEOD-26584 | biostudies-arrayexpress
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile hepatic gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in liver during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with a two-stage mixed model. A total of 905 differentially expressed "functional" genes were identified (FDR<0.10). The greatest number of differentially expressed genes (400) was detected at 7 weeks of age. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines. A balance block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (FL or LL) at six different ages (1, 3, 5, 7, 9 and 11 wk).
2007-08-31 | E-GEOD-8812 | biostudies-arrayexpress
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile pituitary gland gene expression during juvenile development (1 to 7 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia, and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in the pituitary gland during juvenile development using a reference design for the hybridization of total RNA from the pituitary gland. A reference RNA pool was made from an equal amount of high-quality total RNA extracted from all of the samples. Each of the microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the pituitary samples and Cy5-labled cDNA targets from the reference pituitary RNA pool. Log2-transformed fluorescence intensities were analyzed with a mixed model. Two-way ANOVA (SAS) of log2 ratios was used to detect significant (p<0.05) differences by line, age, and the line-by-age interaction. There were 1150 significantly different genes between the two lines, and 339 of these genes exhibited greater than 0.68-fold differences in their log2 ratios (highest group mean at least 160% of the lowest group mean). One thousand four hundred twenty nine genes were significantly different by age and of these, 583 exhibited fold changes greater than 0.68 in the log2 ratio. There were 145 genes that significantly differed in their line-by-age interaction, and 62 of these exhibited greater than 0.68-fold differences. There were 386 genes with significant differences by line or for line-by-age interaction with at least a 0.68-fold change in log2 ratio and n ≥ 2 for each experimental group.
2011-01-13 | GSE26584 | GEO
Project description:Visceral adipose tissue inflammation correlates with metabolic dysfunction in obesity. However, critical cell types that trigger and contribute to inflammation in this depot are not completely understood. Mesothelial cells line the omental fat depot and are thought to contribute to several intraperitoneal inflammatory conditions. Whether adipose-associated mesothelial cell inflammation is a feature of pathologic obesity is unclear. This study was performed to delineate a contribution of omental adipose mesothelial cells to visceral adipose tissue dysfunction in pathologic obesity. We performed a cross-sectional case-control study from two separate cohorts of patients undergoing abdominal surgery with varying degrees of obesity and metabolic disease. Whole-genome expression profiling was conducted on mesothelial cells isolated from lean and obese surgical patients to determine differences in relevant pathways related to obesity and metabolic disease.
2019-03-08 | GSE128021 | GEO
Project description:Background: The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates. Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome. CNV analysis has recently gained greater attention and momentum, as the identification of CNVs can contribute to a better understanding of traits important to both humans and other animals. To detect chicken CNVs, we genotyped 475 animals derived from two broiler chicken lines divergently selected for abdominal fat content using chicken 60K SNP array, which is a high-throughput method widely used in chicken genomics studies. Results: Using PennCNV algorithm, we detected 438 and 291 CNVs in the lean and fat lines, respectively, corresponding to 271 and 188 CNV regions (CNVRs), which were obtained by merging overlapping CNVs. Out of these CNVRs, 99% were confirmed also by the CNVPartition program. These CNVRs covered 40.26 and 30.60 Mb of the chicken genome in the lean and fat lines, respectively. Moreover, CNVRs included 176 loss, 68 gain and 27 both (i.e. loss and gain within the same region) events in the lean line, and 143 loss, 25 gain and 20 both events in the fat line. Ten CNVRs were chosen for the validation experiment using qPCR method, and all of them were confirmed in at least one qPCR assay. We found a total of 886 genes located within these CNVRs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed they could play various roles in a number of biological processes. Integrating the results of CNVRs, known quantitative trait loci (QTL) and selective sweeps for abdominal fat content suggested that some genes (including SLC9A3, GNAL, SPOCK3, ANXA10, HELIOS, MYLK, CCDC14, SPAG9, SOX5, VSNL1, SMC6, GEN1, MSGN1 and ZPAX) may be important for abdominal fat deposition in the chicken. Conclusions: Our study provided a genome-wide CNVR map of the chicken genome, thereby contributing to our understanding of genomic structural variations and their potential roles in abdominal fat content in the chicken.
2015-05-20 | GSE58551 | GEO
Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at Station Recherches Avicoles, Institut National de la Recherche Agronomique Nouzilly, France were used to profile abdominal fat gene expression at 7 weeks of age. The fat line (FL) and lean line (LL) chickens differ in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and triiodothyronine (T3). The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. Massively parallel RNA sequencing (RNA-Seq) was completed on an Illumina HiSeq 2000 System for transcription analysis of FL and LL abdominal fat. Statistical analysis was completed using CLC Genomics Workbench software. A total of 1,703 genes were differentially expressed in the FL versus LL adipose tissue [FDR<0.05 and fold change (FL/LL) > 1.2]. The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors, vasoregulators and transcription factors involved in various pathways. Several of the functional genes identified are also positional candidate genes within quantitative trait loci (QTL) in an F2 population created from an intercross of the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes Abdominal fat mRNA profiles of fat line (FL) and lean line (LL) chickens at 7 weeks of age were generated by deep sequencing (on an Illumina HiSeq 2000 system) employing several sequencing schemes to determine depth of coverage from 1, 4, and 8 multiplexed libraries per sequencing lane. Transcriptional analysis was completed by averaging short paired-end sequence reads (101 bp) for each bird across three sequencing depths.
2013-04-16 | E-GEOD-42980 | biostudies-arrayexpress