Ontology highlight
ABSTRACT:
PROVIDER: PRJNA826088 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18753800_1.fastq.gz | Fastqsanger.gz | |||
| SRR18753800_2.fastq.gz | Fastqsanger.gz | |||
| SRR18753900_1.fastq.gz | Fastqsanger.gz | |||
| SRR18753900_2.fastq.gz | Fastqsanger.gz | |||
| SRR18753801_1.fastq.gz | Fastqsanger.gz |
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Project description:The liver plays a critical role in avian reproduction as it is the primary site of de novo lipogenesis and yolk precursor synthesis. Broiler breeder hens, the parents of commercial broiler chickens, often experience poor reproductive efficiency primarily due to declining egg production beginning around 45 weeks of age. Metformin, an antidiabetic drug, exerts its primary effects in the liver by increasing insulin sensitivity and reducing hepatic glucose production in humans. This study aimed to characterize the liver transcriptomic profile of broiler breeder hens supplemented with metformin in the diet at 0 or 75 mg/kg body weight for 40 weeks (25-65 weeks of age; n=45 hens/treatment). Liver tissue was collected from a subset of hens (n=12 hens/treatment group) at 65 weeks of age, RNA was extracted and sequenced using next-generation sequencing. Differential gene abundance analysis revealed that metformin treatment led to the most significant changes in gene expression, with 552 genes differentially expressed compared to the control group. Further transcriptomic analysis highlighted increased expression of genes related to estrogen-stimulated yolk precursor synthesis, insulin-stimulated de novo lipogenesis, and AMPK-mediated glucose homeostasis. qPCR analysis revealed increased expression of ESR1, APOB, APOV1, VTG2, ADIPOQ, ADIPOR2 and ACACA mRNA and decreased expression of PCK1 mRNA validating the transcriptomic data. Collectively, the present study suggests that metformin supplementation supports prolonged egg production in aging broiler breeder hens by sustaining yolk precursor and fatty acid synthesis that are typically diminished in aging broiler breeder hens.
2025-01-14 | GSE286522 | GEO
Project description:Intense selective breeding of broiler breeds of chickens has resulted in suboptimal egg production in broiler breeder hens. Ad libitum feeding which leads to excessive and disorganized follicular growth exacerbates this reproductive phenotype. One strategy used to improve broiler breeder hen reproductive efficiency is restricted feeding. In this study, we sought to identify transcriptional changes which translate level of dietary intake to increased follicle selection. Broiler breeder hens were raised according to commercial guidelines until 28 weeks of age and then randomly assigned to an ad libitum diet (FF) or continued on a restricted diet (RF) for 6 weeks. Following dietary treatment, granulosa cells from growing 6-8 mm follicles from FF hens (n=3) and RF hens (n=3) were collected, RNA was extracted, and samples were processed for RNA-sequencing on Illumina NextSeq 500. Transcriptomes of granulosa cells from 6-8 mm follicles were sequenced to identify transcriptional differences in the population from which follicles are selected into the preovulatory stage. FastQ files were first processed through trim-galore and reads were aligned to the Galgal6 genome using the RNA-seq aligner, STAR. A cluster analysis using hclust in R identified a FF sample as an outlier and this sample was removed from the analysis. Differential expression analysis was conducted using DeSEQ2 and resulted in 350 differentially expressed genes. Several genes involved in follicle selection were upregulated in prehierarchal follicles of FF hens, suggesting an effect of dietary treatment at early stages in follicle development.
2021-09-23 | GSE175887 | GEO
Project description:Broiler chicken production is crucial to meet the increasing global food demand. Hyperphagic and obese broiler breeder hens have a short production cycle, which is challenged by age-associated egg quality and fertility decline, affecting hatchability. A fertilized egg is a comprehensive set of essential elements to nurture and develop a healthy chick. Egg albumin occupies most of the egg content, which is synthesized and secreted by the magnum. The genetic regulation of albumin biosynthesis in broiler breeder hens and its alteration with age might reveal the genetic marker that will produce quality eggs in subsequent generations. Hence, the objective of the study is to determine the differentially expressed genes (DEGs) and pathways involved in albumin biosynthesis in the magnum (young vs aged). The magnum tissues were collected from the broiler breeder hens at peak production, identified as the young group (35 weeks, N=30), and from the declined production, recognized as the aged group (50 weeks, N=30). Five samples from each group (n=5) were used for RNA sequencing and analyzed to get DEGs and associated pathways. The significantly upregulated genes with a putative function in quality egg formation were confirmed using qPCR. Seventy-five up-regulated and 52 down-regulated genes were determined. The top 20 most upregulated genes and top 20 most downregulated genes, based on their putative function, were categorized into five groups: egg white synthesizing (AMDHD1, FER, CTNNA3), molecular communication (VAPA), oviduct tissue regeneration (ADAM19, CFAP100, AMD1, TM4SF19, SLC39A13, VMO1), and defense (ZBTB46, STAM2, OVoDA3). “Post-translational protein phosphorylation” was the most significantly enriched Reactome pathway involving DNAJC3, PPP3CA, TF, SPARCL1, PDIA6, SGPP2, HSP90B1, and PNPLA2 genes. The study successfully identified DEGs, genetic networks, and pathways that can be used as genetic markers to select quality egg producing broiler breeder hens.
2025-05-16 | GSE296459 | GEO
Project description:Sperm storage tubules (SSTs) in the uterovaginal junction (UVJ) of the oviduct are major sites of sperm storage after artificial insemination or mating. Female birds may regulate sperm motility in the UVJ. Heat stress can decrease the reproductive ability of broiler breeder hens. However, its effects on UVJ remain unclear. Changes in gene expression aid in understanding heat stress-affected molecular mechanisms. Herein, we wanted to conduct a comparative transcriptomic analysis to identify the differentially expressed genes (DEGs) in the UVJ of breeder hens under thermoneutral (23°C) and heat stress (36°C for 6 h) conditions.
2025-04-28 | GSE295785 | GEO
Project description:Ovarian dysfunction is observed in broiler breeder hens fed ad libitum that is most apparent by a reduction in fertility success. Restricting caloric intake in these hens is currently the only effective treatment to improve reproductive efficiency. This analysis sought to determine the transcriptional changes in the ovarian cortex of prepubertal hens given full access to feed (FF) or were placed on a restricted feed (RF) diet. Microarrays were employed to detail the differences in global gene expression that underlie the ovarian dysfunction observed in ad libitum fed hens.
2021-09-15 | GSE184105 | GEO
Project description:Heat stress (HS) can damage the integrity of the intestinal mucosal barrier, leading to decreased poultry productivity. This study aimed to identify candidate genes related to acute HS in breeder hens and provide insight into the molecular mechanisms underlying acute HS in gut health. Fifty 28-week-old breeder hens were divided into two groups (25 hens each) raised under thermoneutral zone (23 °C) and acute HS (36 °C, 6 hours) conditions. The heart rate and cloacal temperature were measured in all hens, and jejunal mucosa tissues were randomly collected from 12 hens per treatment for RNA-sequencing analysis. The results indicated a significant increase in the heart rate and cloacal temperature in hens exposed to acute HS (P < 0.05). Transcriptome analysis identified 138 differentially expressed genes (DEGs) in heat-stressed breeder hens, including 75 upregulated DEGs containing heat shock protein (HSP), energy homeostasis metabolism-related gene (PDK4), and fat metabolism-related genes (PPARA and CD36), and 63 downregulated DEGs containing the bile acid transporter gene (SLC10A2). Gene ontology analysis revealed significant enrichment in biological processes related to heat response and cholesterol biosynthesis. Kyoto Encyclopedia of Genes and Genomes analysis highlighted several significant pathways, including steroid biosynthesis, steroid hormone biosynthesis, protein processing in endoplasmic reticulum, the peroxisome proliferator-activated receptor (PPAR) signaling pathway, and the adipocytokine signaling pathway. Protein-protein interaction network analysis involving two large networks: one containing several upregulated HSPs and genes related to energy homeostasis and fat metabolism (PDK4, PPARA, and CD36) and glucose transporter (SLC2A5), and the other containing downregulated DEGs related to cholesterol biosynthesis. Overall, acute HS might affect energy metabolism, fat metabolism, and glucose transport in the jejunal mucosa of breeder hens. Heat-stressed hens could restore the nutritional function of the jejunal mucosa by increasing the expression of HSPs. These findings provide a theoretical framework for further investigation into the molecular regulatory mechanisms responsible for HS-induced changes in the gut health of poultry.
2024-12-18 | GSE279179 | GEO
Project description:Broiler breeder hens given ad libitum access to feed have excessive ovarian follicle development with poor reproductive outcome. One strategy to improve their reproductive capacity is by restricting their feed intake. In this study, we sequenced the liver transcriptomes of hens fed ad libitum (FF, n=3) and hens given a restricted fed diet (RF, n=3) to get insight into possible signaling pathways affected by dietary treatment. Hens were reared according to commercial guidelines until 38 weeks of age, when they were assigned to either FF or continued on RF for 6 weeks. Liver mRNA samples from three hens in each group were sequenced using the Illumina HiSeq 2000/2500 technology at a depth of 100 bp. The sequencing quality of the data was determined using FastQC. Reads were aligned to UCSC Galgal4 using Tophat (v2.0.13) and transcripts were counted using cuffdiff (v.2.2.1). A multidimensional scaling plot (MDS plot) was generated to evaluate the variance among biological replicates and identified one FF hen as a sample outlier and this animal was removed from the analysis. Differential gene expression analysis was conducted using edgeR and yielded 120 differentially expressed genes. This study identified transcriptional differences in the livers of FF and RF hens which may signal metabolic status to the ovary.
2022-02-03 | GSE175780 | GEO
Project description:The egg production cycle of broiler breeder hens is comparatively shorter than laying hens, and as they age, their egg production and eggshell quality decline. The eggshell formation occurs in the shell glands, which are influenced by several factors, including aging. The objectives of the study were to 1) identify differentially expressed genes (DEGs) and biological pathways in the shell glands (young vs aged) and 2) determine the age-associated changes in eggshell quality. The shell glands tissues were collected from broiler breeder hens at peak-lay (35 weeks of age; termed as “young”) and late-lay phases (50 weeks of age; termed as “aged”) (n=30/group) at 10-15 hours post-ovulation (unclassified egg present in the shell glands). To delineate the genes and biological pathways associated with eggshell biomineralization, total RNAs extracted from the shell glands of young and aged hens (n=6/group) were analyzed using RNA sequencing and validated using real-time PCR. The ultrastructure quality of eggshells (n=10 eggs/group) was analyzed using a Scanning Electron Microscope (SEM), and the elemental composition of eggshells was measured using SEM-Energy Dispersive Spectrometry, and their variability was confirmed by t-test in RStudio. Eggshell strength, thickness, palisade layer, and mammillary width were significantly higher in the young, while mammillary knobs were wider in aged hens (p<0.05). The sulfur and potassium levels in eggshells were higher in young hens than aged ones. Although the young group had a higher calcium concentration in the eggshells, the difference was statistically insignificant (p>0.05). RNA-Seq data identified highly upregulated genes specific to eggshell biomineralization, such as SPP1 (binds to hydroxyapatite), OTOP2 (maintains high conc. of cytosolic Ca2+), PKD2 (helps in releasing Ca2+), SLC22A15 (transports organic ions), and STAB2 (binds to gram-positive and gram-negative bacteria). The DEGs showed significant enrichment for biological pathways (SLC6A6, KCNK7, UCP3, SCNN1A, PKD2, OTOP2) associated with the transport of monoatomic and inorganic cations across the cell membrane, molecular functions related to the transport of potassium ions and the activity of monoatomic cation channels (KCNK7, PKD2, OTOP2), and the cellular components involved in the luminal side of the endoplasmic reticulum membrane (CALR, PKD2). These findings suggest that the aging process downregulates the transcriptomes of the shell glands, negatively impacting the transportation of ions required for eggshell formation, resulting in poor eggshell quality.
2025-05-12 | GSE296109 | GEO
Project description:Overfeeding reduces laying performance in broiler breeder hens (Gallus gallus domesticus). To unravel the effect of feeding regimes on energy metabolism and egg production, high-throughput RNA sequencing was utilized to identify differentially expressed genes (DEGs) in ovary, liver and adipose tissues of broiler chickens under ad libitum and restricted feeding. The transcriptome analysis showed that 289, 388 and 204 DEGs were identified in the adipose tissue, liver and ovary, respectively, between ad libitum and restricted feeding groups. Bioinformatics analysis by STRING further revealed DEGs were significantly enriched in phagosome pathway, lipid transport and location biological process, and the molecular function of lipid transporter activity and nutrient reservoir activity in ovary; the pathways of “steroid hormone biosynthesis” and “metabolism of xenobiotics by cytochrome P450”, and the molecular function of nutrient reservoir activity in adipose tissue; the metabolic pathways, Jak-STAT signaling pathway and PPAR signaling pathway in liver.
2019-05-08 | GSE113722 | GEO
Project description:In vitro gut microbiota models are often used to study drug-microbiome interaction. Similar to culturing individual microbial strains, the biomass accumulation of in vitro gut microbiota follows a logistic growth curve. Current studies on in vitro gut microbiome responses introduce drug stimulation during different growth stages, e.g. lag phase or stationary phase. However, in vitro gut microbiota in different growth phases may respond differently to a same stimuli. Therefore, in this study, we used a 96-deep well plate-based culturing model (MiPro) to culture the human gut microbiota. Metformin, as the stimulus, was added at the lag, log and stationary phases of growth. Microbiome samples were collected at different time points for optical density and metaproteomic functional analysis. Results show that in vitro gut microbiota responded differently to metformin added during different growth phases, in terms of the growth curve, alterations of taxonomic and functional compositions. The addition of drugs at log phase leads to the greatest decline of bacterial growth. Metaproteomic analysis suggested that the strength of the metformin effect on the gut microbiome functional profile was ranked as lag phase > log phase > stationary phase. Our results showed that metformin added at lag phase resulted in a significantly reduced abundance of the Clostridiales order as well as an increased abundance of the Bacteroides genus, which was different from stimulation during the rest of the growth phase. Metformin also resulted in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.
2022-03-01 | PXD017390 | Pride