Ontology highlight
ABSTRACT:
PROVIDER: PRJNA782769 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17032375_1.fastq.gz | Fastqsanger.gz | |||
| SRR17032375_2.fastq.gz | Fastqsanger.gz | |||
| SRR17032376_1.fastq.gz | Fastqsanger.gz | |||
| SRR17032376_2.fastq.gz | Fastqsanger.gz | |||
| SRR17032377_1.fastq.gz | Fastqsanger.gz |
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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.
2018-12-06 | GSE114103 | GEO
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.
2021-03-22 | GSE123588 | 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:<p>Background The intestinal microbiota, metabolites, and quorum-sensing (QS) functions of laying hens under different proportions of fermented Cordyceps militaris mushroom substrate (CMMS) replacement diets are critical for their production performance and health. However, the changes in the intestinal microbiota, metabolites, and QS functions of laying hens under different proportions of fermented CMMS replacement diets, as well as their effects on laying hen production performance, remain unclear. This study evaluated the changes in production performance, apparent digestibility, digestive enzyme activity, serum immunoglobulin levels, cecal microbiota and metabolites, and QS function of laying hens under different proportions of fermented CMMS replacement diets, as well as their impact on the health of laying hens.</p><p>Results Using Hymenoptera brown egg-laying chicken as the research subject, this study aimed to determine the production performance, egg quality, apparent digestibility, digestive enzyme activity, and serum immunoglobulin levels of egg-laying chickens under different ratios of fermented CMMS replacement diets. Additionally, the study analyzed the cecal microbiome and metabolome. The dry matter, neutral detergent fiber, and phosphorus content of CMMS significantly decreased after fermentation treatment (P < 0.05). When 30% of the diet was replaced with fermented CMMS, the laying rate, average egg weight, average daily feed intake, and feed-egg ratio significantly increased (P < 0.05). Egg yolk color and Haugh unit significantly increased (P < 0.05), and lipase significantly increased (P < 0.05). When 20% of the diet was replaced with fermented CMMS, the apparent digestibility of DM, CP, ash, and NDF in laying hens significantly increased (P < 0.05), and IgA and IgM significantly increased (P < 0.05). Metagenome analysis showed that when fermented CMMS replaced 30% of the diet, the relative abundance of Phocaeicola, Alistipes, and Parabacteroides significantly increased (P < 0.05), Kyoto Encyclopedia of Genes and Genomes (KEGG) level 2 pathway energy metabolism increased, and QS pseudouridine-synthase RluA family genes increased. A total of 1,529 differentially expressed metabolites were identified under different proportions of fermented CMMS replacement diets. The highest relative content was found in carboxylic acids and derivatives (21.20%), and taurine and hypotaurine metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis were enhanced. When fermented CMMS replaced 30% of the diet, the relative abundance of Parabacteroides significantly increased (P < 0.05) and was significantly negatively correlated with tetradecanedioic acid and sebacic acid (r < 0, P < 0.001). The relative abundance of Alistipes significantly increased (P < 0.05) and was significantly positively correlated with the PemK/MazF family (r > 0, P < 0.001).</p><p>Conclusions The relationship between the microbial community in the cecum of laying hens, its metabolites, and QS function under different proportions of fermented CMMS replacement diets, as well as their regulation of production performance, apparent digestibility, and immune levels. It determined their potential impact on the metabolism and health of laying hens. The research results provide valuable insights into the potential of CMMS as an unconventional feed.</p>
2025-09-09 | MTBLS12825 | MetaboLights