Ontology highlight
ABSTRACT:
PROVIDER: PRJNA664592 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12681000_1.fastq.gz | Fastqsanger.gz | |||
| SRR12681000_2.fastq.gz | Fastqsanger.gz | |||
| SRR12681001_1.fastq.gz | Fastqsanger.gz | |||
| SRR12681001_2.fastq.gz | Fastqsanger.gz | |||
| SRR12681002_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Even though feather pecking (FP) in laying hens has been extensively studied, a good solution to prevent chickens from this behavior under commercial circumstances has not been found. Selection against FP behavior is possible, but for a more effective selection across different populations, it is necessary to characterize the genetic mechanism associated with this behavior. In this study, we use a high FP selection line, which has been selected for 8 generations. We present evidence of the presence of a major dominant allele affecting the FP behavior by using an argument based on the presence of mixture in the distribution of the observed FP and by studying the evolution of the proportion of very high FP along the sequence of 8 generations. This hypothesis is further supported by the fact that the gene transcription profile of the birds performing high FP differs from the profile of the other birds performing FP (456 genes differentially expressed from a total of 14,077 investigated genes). Keywords: severe feather pecking , selection , modeling , inheritance pattern From each selection line (high feather pecking line, low feather pecking line and control line) 60 animals were randomly selected. Within each line the birds were randomly assigned to a cage of 20. The cages were kept in a randomized block design. Number of samples analyzed in total: 179 (60 high feather pecking line, 60 low feather pecking line, 59 control line samples. Common reference design using total-RNA purified from brain from a single F1 cross between the high and low feather pecking line as reference.
2009-09-22 | E-GEOD-10380 | biostudies-arrayexpress
Project description:Even though feather pecking (FP) in laying hens has been extensively studied, a good solution to prevent chickens from this behavior under commercial circumstances has not been found. Selection against FP behavior is possible, but for a more effective selection across different populations, it is necessary to characterize the genetic mechanism associated with this behavior. In this study, we use a high FP selection line, which has been selected for 8 generations. We present evidence of the presence of a major dominant allele affecting the FP behavior by using an argument based on the presence of mixture in the distribution of the observed FP and by studying the evolution of the proportion of very high FP along the sequence of 8 generations. This hypothesis is further supported by the fact that the gene transcription profile of the birds performing high FP differs from the profile of the other birds performing FP (456 genes differentially expressed from a total of 14,077 investigated genes). Keywords: severe feather pecking , selection , modeling , inheritance pattern
2009-09-22 | GSE10380 | GEO
Project description:Feather pecking is a major welfare problem in egg production. It may be caused by genetic, physiological and environmental factors. The main aim of this study was to uncover variability in gene expression between individuals from high (HFP) and for low feather pecking (LFP) line using Chicken Gene Expression Microarrays (Agilent Technologies). Samples were assorted to two groups, each containing 9 biological replicates from high feather pecking (HFP) and low feather pecking (LFP) line.
2012-03-17 | E-GEOD-36559 | biostudies-arrayexpress
Project description:Differences in the gut microbial composition of divergently selected laying hen lines does not affect feather pecking and agonistic behavior
| PRJEB40535 | ENA
Project description:Feather pecking is a major welfare problem in egg production. It may be caused by genetic, physiological and environmental factors. The main aim of this study was to uncover variability in gene expression between individuals from high (HFP) and for low feather pecking (LFP) line using Chicken Gene Expression Microarrays (Agilent Technologies).
2012-03-17 | GSE36559 | GEO
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:Analysis of severe feather pecking behavior in a high feather pecking selection line
| PRJNA108119 | ENA
Project description:Calcium (Ca) and phosphorus (P) are essential micronutrients that are linked to a wide set of biological processes. In laying hens there is still uncertainty about the optimal Ca/P ratio in feed and further strategies for the reliable mineral restriction in poultry diets are required. The dataset is based on Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) laying hens sampled at peak performance. The experimental design comprises four dietary groups 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 low P diet (LP). Jejunal transcriptome profiles were assessed by mRNA sequencing in a total of 80 animals (10 hens per experimental group for each laying line) at sampling age of 31 weeks) to approximate the consequences of variable Ca and P supply.
2021-06-14 | E-MTAB-9109 | biostudies-arrayexpress