Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1200904 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31817248.fastq.gz | Fastqsanger.gz | |||
| SRR31817249.fastq.gz | Fastqsanger.gz | |||
| SRR31817250.fastq.gz | Fastqsanger.gz | |||
| SRR31817251.fastq.gz | Fastqsanger.gz | |||
| SRR31817252.fastq.gz | Fastqsanger.gz |
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Project description:Selective breeding in laying hens has resulted in a laying rate of approximately one egg per day during their first year. Due to variability within a flock, this rate declines after the first year, leading producers to cull hens. The aim of this study was to identify physiological and molecular differences between persistent (PL, egg-laying rate = 100%) and non-persistent layers (NPL, egg-laying rate ≤ 82%) after the first year. Forty laying hens were reared from 16 to 76 weeks of age and a subset was maintained until 96 weeks. Throughout the study, egg-laying data were recorded daily. At 76 weeks, ovarian tissue was collected from PL (n=3) and NPL (n=4) hens for RNA-sequencing. Ovarian RNA-sequencing analysis revealed 279 differentially expressed genes between PL and NPL hens and analysis predicted the estrogen receptor as an upstream regulator. A greater understanding of the physiology and molecular patterns of persistent hens could enhance production efficiency and provide insights into ovarian aging in women.
2026-04-01 | GSE294546 | GEO
Project description:<p>Lactobacillus has antioxidant properties that may benefit poultry production. However, there is no systematic research on antioxidant of Lactobacillus strain and its effects on regulating nutrient metabolism in aged laying hens. This study investigated the influence of Leuconostoc lactis on production and antioxidant capacity in aged laying hens and explored the key biomarkers associated with tryptophan-skatole metabolism and its effects on the intestinal microbiota-liver axis. Hens supplemented with L. lactis showed a higher laying rate, reduced hepatic MDA levels, and increased T-AOC in comparison with the control group (CG). Indole-3-acetaldehyde (IAld) levels were elevated in both feces and yolk, and skatole decreased in feces by the L. lactis group compared to CG. The total polyunsaturated fatty acids (PUFAs), C18:3n3, and C18:2n6c in yolk were raised in the L. lactis group relative to CG. In the liver, mRNA levels of AhR, CYP2D6, and CPT-1 were markedly upregulated in the L. lactis group relative to CG. The L. lactis-treated group also exhibited higher alpha diversity in fecal samples at 30 days and in ileal samples at 60 days. Further, we conducted the hepatocyte validation experiment and found that MDA levels were significantly reduced, and T-AOC was increased in both the L. lactis and IAld-treated groups compared with the CG. IAld treatment significantly affected p38, and NF-κB, and Nrf2 cytokine expression in hepatocytes. The findings provide a reference for the use of L. lactis in improving production and intestinal nutrition in aged laying hens.</p>
2025-09-09 | MTBLS12964 | MetaboLights
Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide variety of tissues has been discovered. The aim of this study are to perform uterine transcriptome profiling (RNA-seq) to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR) in laying, non-laying and molting hens. Methods: Uterine mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least two-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed. Results: Using an optimized data analysis workflow, we mapped about 32 million reads from layers and 28 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 616 were differentially expressed between layer and non-layer hens. 229 DEGs were significantly up-regulated and 286 were significantly down-regulated in the laying hens when compared to the non-laying hens. Twelve candiate genes, linked to calcium remodeling, were identified by gene function analysis and validated using qPCR. MEPE, CALCB, OTOP2, STC2 and ATP2C2 were confirmed to be highly expressed in laying hens as compared to molting and non-laying hens. RNA-seq and qPCR data for relative gene expression were highly correlated (R2 =0.99). Conclusions: Our study reports the expression of four novel genes that are speculated to transport calcium ions across the uterine epithellium for eggshell mineralization. These genes can be used as quantitative basis of selecting hens with an improved eggshell quality.
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Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide varitey of tissues has discovered. The aim of this study are to perform transcriptome profiling (RNA-seq) of magnum to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR) in laying, non-laying and molting hens. Methods: Magnum mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least three-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed. Results: Using an optimized data analysis workflow, we mapped about 30.5 million reads from layers and 33.4 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 540 were differentially expressed between layer and non-layer hens. 152 DEGs were significantly up-regulated and 388 were significantly down-regulated in the laying hens when compared to the non-laying hens. Conclusions: Our study reports the expression of several pre-discovered and many novel genes that may be involved in the transport of precurosor molecules for biosynthesis and secretion of the egg-white proteins in the magnum. These genes can be used as quantitative basis of selecting hens with an improved egg quality.
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Project description:In this study, we deep-sequenced the transcriptomic profile of the ileum mucosa in two laying hen strains (Lohmann Brown-Classic and Lohmann LSL-Classic) at 10, 16, 24, 30, and 60 weeks of age. These five time points span the initial, peak and end of the lay periods in which the hens critically experience physiological changes and need optimal diets to meet both growth and egg production requirements. Therefore, a comparative transcriptome profiling of the ileum mucosa may lead to a better understanding of molecular mechanisms underlying genetics, age and nutrition factors of layers.
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Project description:Calcium (Ca) and phosphorus (P) are essential micronutrients linked to arrays of biological processes and physiological conditions. In laying hens, the optimal Ca/P ratio in feed is inconsistent but necessary for reliable schemes of mineral restriction in poultry diets. This study investigates the effects of dietary treatments varying in the Ca and P levels in two laying hen strains (Lohmann Brown-Classic and Lohmann LSL-Classic) at the peak of egg production (31 weeks of age). Four dietary treatment groups were differed in Ca (recommended vs. 15 % reduction) and mineral P (adequate vs. 20 % reduction) levels; 1) control diet (Con; Ca=34.4g/kg, P=5.3 g/kg and Ca/P ratio=7.45), 2) Low Ca and P diet (LCaP), 3) low Ca diet (LCa), and 4) low P diet (LP). microRNA expression of the jejunum mucosa were profiled by microRNA sequencing in a total of 80 animals (10 hens per experimental diet group for each of the two laying line) at sampling age of 31 weeks. RNA-seq data of matched samples are also available (E-MTAB-9109).
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