Liver transcriptome of sexually mature hens in relation to the formation of the egg yolk
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
SUBMITTER: Joel Gautron
PROVIDER: E-GEOD-35595 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We used a transcriptomic approach based on the comparison of the expression between the liver of sexually mature hens versus pre-laying pullets to better appreciate which hepatic proteases and antiproteases are specifically expressed in relation to vitellogenesis. Using a 20K chicken oligoarray corresponding to 12 595 different chicken genes, a total of 582 genes were shown to be over-expressed in the liver at sexual maturity of hens (1.2 to 67 fold- difference). Most of the top ten over-expressed genes are known components of egg yolk or of the perivitelline membrane. The combination of different bioinformatic tools reveals 12 proteases and 3 antiproteases amongst the over-expressed genes, including many predicted proteins with yet unknown functions.
2012-04-01 | GSE35595 | 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 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:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P ⤠0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change ⥠2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR ⤠0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ⤠0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver. The liver expression profile of juvenile hens and laying hens were generated by RNA-seq.
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Project description:Transcriptional profiling of eight normal adult chicken tissues in 10-week old brown (lohmann brown) hens, the eight tissues include brain, bursa of Fabricius, jejunum, kidney, liver, lung, spleen, thymus. Keywords: normal chicken tissues, transcriptional profiling.
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Project description:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P ≤ 0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change ≥ 2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR ≤ 0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ≤ 0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver.
2016-01-08 | GSE70010 | GEO
Project description:Hepatic steatosis is the initial manifestation of abnormal liver functions and often leads to liver diseases such as non-alcoholic fatty liver disease in humans and fatty liver syndrome in animals. In this study, we conducted a comprehensive analysis of a large chicken population consisting of 705 adult hens by combining host genome resequencing, liver transcriptome, proteome, and metabolome analysis, as well as microbial 16S rRNA gene sequencing of each gut segment.
2024-04-09 | PXD042451 | Pride
Project description:Chickens divergently selected for either high growth (HG genotype) or low growth (LG genotype) by F.H. Ricard at SRA-INRA, Nouzilly France were used for time-course transcriptional profiling of abdominal fat during juvenile development (1 to 11 weeks of age) to identify differentially expressed genes. The HG and LG chickens are different in various phenotypic and metabolic measurements, including growth rate, abdominal fat, plasma glycemia, insulinemia, T4, T3, triglyceride and NEFA. Thus, the HG and LG chickens are valuable as a model for biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in abdominal adipose during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with the linear mixed model (MIXED) procedure in SAS (SAS Institute Inc., Cary, NC, USA). A total of 3,957 differentially expressed functional genes were identified (FDR<0.05) as having a significant effect of age (2,918), genotype (312), or an age by genotype interaction (727). The differentially expressed genes include adipokines, metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors and transcription factors involved in various pathways. Keywords: abdominal fat, divergently selected chickens, growth, transcriptional profiling, differentially expressed genes, lipogenesis A balanced 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 (HG or LG) at six different ages (1, 3, 5, 7, 9 and 11 wk).
2013-04-06 | E-GEOD-45825 | biostudies-arrayexpress
Project description:cDNA microarrays were used to identify the expression of the genes in uterus by comparison with two others regions of the oviduct not involved in the shell deposition. A total of 605 sequences specifically over-expressed were revealed. The expression of 15 of them was also confirmed using qRT-PCR, and confirmed the microarray expression. The 605 uterine transcripts corresponded to 469 and 437 different genes and proteins respectively. A global interpretation of their functions was assessed using the Gene Ontology terms and the most over-represented terms are relative to the mineral transport and transfer necessary to the calcification process. The study has revealed 53 proteins which could be secreted to be deposited in the shell to be biologically actives. The study of their functions reveals proteins known for their involvement in the biomineralization or with calcium binding properties to interact with the mineral phase during the eggshell fabric. A large group of proteins could be involved in the folding of the matrix, and a notable group of uterine secreted proteins was also identified as antibacterial to contribute to the antimicrobial protection of the egg. Finally the study revealed proteases and protease inhibitors which could play an active role in the regulation of the protein activities in the acellular uterine fluid where the eggshell is formed. Keywords: Laying hen, eggshell, oviduct, uterine expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes A balanced block hybridization design (Dye switch) was used where half of the samples were labelled with Alexa® 555 fluorescent dye and the other half with Alexa® 647. A total of 16 microarray slides were used for hybridization to 32 samples that correspond to four tissue contrast (uterus versus magnum and uterus versus white isthmus).
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Project description:Exposure to environmental contaminants like nonylphenol can disrupt smolt development and may be a contributing factor in salmon population declines. We used GRASP 16K cDNA microarrays to identify genes that are differentially expressed in the liver, gill, hypothalamus, pituitary, and olfactory rosettes of Atlantic salmon smolts treated with nonylphenol compared to control smolts. Nonylphenol treatment was confirmed using physiological assays: nonylphenol-treatment significantly decreased gill Na+,K+-ATPase activity and plasma cortisol and T3 levels. Microarray analyses were used to compare expression in nonylphenol-injected fish with expression in vehicle-injected fish: eight arrays each for liver, gill, olfactory rosettes, hypothalamus, and pituitary tissues. Total RNA was isolated from the tissues of eight nonylphenol-injected fish (six males and two females) and eight vehicle-injected fish (two males and six females) and reverse transcribed separately (not pooled); each slide represents a biological replicate. For each tissue, the eight arrays were balanced for dye: nonylphenol-injected fish were labeled with Alexa Fluor 555 and vehicle-injected fish were labeled with Alexa Fluor 647 on four slides, nonylphenol-injected fish were labeled with Alexa Fluor 647 and vehicle-injected fish were labeled with Alexa Fluor 555 on four slides. Liver, gill, hypothalamus, pituitary, and olfactory rosette tissues were analyzed separately.
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