Gallus gallus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA393834 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5817520_1.fastq.gz | Fastqsanger.gz | |||
| SRR5817520_2.fastq.gz | Fastqsanger.gz | |||
| SRR5817521_1.fastq.gz | Fastqsanger.gz | |||
| SRR5817521_2.fastq.gz | Fastqsanger.gz | |||
| SRR5817522_1.fastq.gz | Fastqsanger.gz |
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Project description:Duration of fertility, (DF) is an important functional trait in poultry production and lncRNAs have emerged as important regulators of various process including fertility. In this study we applied a genome-guided strategy to reconstruct the uterovaginal junction (UVJ) transcriptome of 14 egg-laying birds with long- and short-DF (n = 7); and sought to uncover key lncRNAs related to duration of fertility traits by RNA-sequencing technology. Examination of RNA-seq data revealed a total of 9977 lncRNAs including 2576 novel lncRNAs. Differential expression (DE) analysis of lncRNA identified 223 lncRNAs differentially expressed between the two groups. DE-lncRNA target genes prediction uncovered over 200 lncRNA target genes and functional enrichment tests predict a potential function of DE-lncRNAs. Gene ontology classification and pathway analysis revealed 8 DE-lncRNAs, with the majority of their target genes enriched in biological functions such as reproductive structure development, developmental process involved in reproduction, response to cytokine, carbohydrate binding, chromatin organization, and immune pathways. Differential expression of lncRNAs and target genes were confirmed by qPCR. Together, these results significantly expand the utility of the UVJ transcriptome and our analysis identification of key lncRNAs and their target genes regulating DF will form the baseline for understanding the molecular functions of lncRNAs regulating DF.
2018-02-14 | GSE101163 | GEO
Project description:Avian uterine fluid (UF) and uterovaginal sperm storage tubules (SST) are key components for acceptance of sperm in SST, sperm functions maintenance during weeks, sperm release out of SST, and their ascending through the uterus. The study of UF and SST is essential to better understand sperm storage process. The objectives were to identify proteins modulated in the hen’s oviduct by sperm, and to highlight their role during sperm storage. Two genetic lines of hens exhibiting long (F+) or short (F-) sperm storage ability were used. GeLC-MS/MS strategy was used to establish a quantitative inventory of proteins regulated after insemination in both lines. Consequently the identification of high (ANXA4/ANXA5/OCX32) and low (HSPA8/PIGR) fertility markers was investigated in uterovaginal junction by immunohistochemistry. Our results demonstrated that sperm induced a significant and rapid change in the UF proteomic content, as well as in the SST epithelium. In F+ hens, the ANXA4 protein mobilization in apical part of SST cells after insemination was associated to increased levels of some proteoglycans and binding proteins, as well as antimicrobial eggshell matrix protein (OCX32) in the UF. We also observed increased levels of lipid transporters involved in egg formation (VTG1-2, APOA1-4-H). In F- hens, insemination induced increased levels of PIGR in both UF and SST, of ANXA5 in SST, of UF enzymes exhibiting metallopeptidase activity, and mucins. In conclusion, sperm induced significant changes in the UF proteomic content. This study also provides evidence that the SST immune system is major to regulate sperm storage.
2019-08-29 | PXD013514 | Pride
Project description:TMT labeled proteome and acetylated proteome were used to reveal molecular mechanisms adapting to the physiological changes between pre- and peak-laying hens
2022-02-17 | PXD024718 | Pride
Project description:Effects of intestinal environment on egg production in laying hens
| PRJDB10504 | ENA
Project description:miRNA expression profiling in liver of juvenile and egg-laying hens
| PRJNA299589 | ENA
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: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:<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
Project description:The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development. A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance. We use 4 different hen lines:; - one line of laying hens with 3 different samples: the just ovulated oocyte, the oocyte collected 24 hours before ovulation (F1 stage), and granulosa cells collected at the F1 stage. We could compare different tissue and developmental stages. - one line of hen with rapid growth speed; - two lines of laying hens; For the 3 last lines we used animals with different fertility levels. We collected the oocyte of the largest follicle before ovulation (F1). The aim of the study is to identify genes involved in fertility or early embryo mortality. Experiment Overall Design: 6 arrays - Gallus gallus
2008-11-08 | E-GEOD-7805 | biostudies-arrayexpress