Gallus gallus
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB10504 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR244385_1.fastq.gz | Fastqsanger.gz | |||
| DRR244385_2.fastq.gz | Fastqsanger.gz | |||
| DRR244386_1.fastq.gz | Fastqsanger.gz | |||
| DRR244386_2.fastq.gz | Fastqsanger.gz | |||
| DRR244387_1.fastq.gz | Fastqsanger.gz |
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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
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Project description:miRNA expression profiling in liver of juvenile and egg-laying hens
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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: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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Project description:This study investigated changes in gut transcriptome in response to the removal and reduction P (0 and 1 g P/kg feed) during the transition to egg production (at 19 and 24 weeks, before and after the onset of laying) in Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) chickens. A total of 80 LB and LSL hens were sampled in a 2x2x2 factorial design, encompassing two strains, age groups, and dietary.
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Project description:The intestinal mucosa is the main organ that exerts nutrient absorption, which will further influence laying performance and egg nutrition in hens. Previously, we have screened out three strains of Lactobacillus (L. sa., L. ag. and L. av.) from a native chicken breed in China. However, the optimal regulation of Lactobacillus combination on poultry products needs to be verified. In this study, a total of 120 HyLine hens (n = 30) at the period of laying peak were randomly divided into four groups: (1) control, (2) L. sa. + L. ag., (3) L. sa. + L. av. and (4) L. ag. + L. av. groups, which were fed with corresponding Lactobacillus (10e8 CFUs/hen/day) for 30 consecutive days. Compared with the control group, feeding of L. sa. + L. ag. could improve the laying rate, egg weight, especially for higher amino acids level in albumen. The mechanism study showed that, in the intestine lumen, feeding of L. sa. + L.ag. could up-regulate the Lactobacillus abundance and down-regulate the Escherichia coli abundance. Meanwhile, the tryptophan metabolism pathway was up-regulated, the primary bile acid biosynthesis pathway was down-regulated. In the crypt, up-regulated genes involved the oxidative phosphorylation pathway and the ROS level were appeared in L. sa. + L.ag. feeding group. Our study further proved that the amount of Paneth cells and the mRNA abundance of Wnt3a and Dll1 in the crypt were up-regulated upon L. sa. + L. ag. feeding. Correspondingly, the mRNA abundance of Lgr5, CCND1 and CDK2 in the crypt were enhanced upon L. sa. + L. ag. feeding. In conclusion, co-feeding of L. sa. and L. ag. in hens could improve the gut microflora and altered the microflora metabolism profile in the intestine. Further, promote the crypt’s local energy metabolism and enhancing ROS level in the crypt, thereby enhance the activity of Paneth cell and regulate the activity of ISCs. Ultimately, the intestinal mucosal renewal and the laying performance were improved.
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Project description:broody and egg-laying Chinese Chahua chickens transcriptome
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Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 8,413 nuclei in chicken adult testis. This dataset includes two samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
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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.
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