Anas platyrhynchos
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA392032 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5759660.fastq.gz | Fastqsanger.gz | |||
| SRR5759661.fastq.gz | Fastqsanger.gz | |||
| SRR5759662.fastq.gz | Fastqsanger.gz | |||
| SRR5759663.fastq.gz | Fastqsanger.gz | |||
| SRR5759664.fastq.gz | Fastqsanger.gz |
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Project description:Background: Skeletal muscle growth and development is highly orchestrated in gene expressions. Understanding the location-specific and breed-specific genes and pathways are agriculturally important on meat products and meat quality. In the present study, RNA-Seq was performed to elucidate the difference of muscle deposition between locations and breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected for pectoral muscle (PM) and leg muscle (LM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared location-specific genes between PM and LM, while Experiment 2 compared the two breeds (H and P) at the same development stage (embryonic 15 days). Results: Almost 13 million clean reads was generated using Illumina technology on each library, and more than 70% reads mapped to Anas platyrhynchos breed Peking duck genome. We identified 246, 258, 20 and 54 differentially expressed genes (DEGs) (log2.fold-change >0.5, and P-value <0.05) for H-PM vs H-LM, P-PM vs P-LM, H-LM vs P-LM and H-PM vs P-PM library, separately. A total of 168 genes were differentially expressed by over locations in experiment 1, while only 8 genes were differentially expressed by over breeds in experiment 2. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DGEs. In experiment 1, DEGs mainly involved in Focal adhesion, PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05). In experiment 2, DEGs only associated with ribosome signal pathway (corrected P-value<0.05). In addition, quantitative real-time PCR was employed to confirm 15 differentially expressed genes detected by RNA-Seq. Conclusions: Comparative transcript analysis of leg muscle and pectoral muscle of two duck breeds not only improves our understanding of those location-specific and breed-specific genes and pathways, but also provides some candidate molecular targets for increase muscle products and meat quality by genetic control. Conclusions: Our study represents the first detailed analysis of duck breed muscle transcriptomes generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2015-12-30 | GSE65628 | GEO
Project description:Purpose:To understand the transcriptome regulator of duck spleen infected with duck enteritis virus (DEV).Methods:50-day-old ducks were inoculated with 100 titer (The TCID50 of DEV was 10-9/0.1mL) and 10-2 titer two different viral titer of DEV in leg muscle for different durations (66 h, 90 h and 114 h) and seronegative control (0 h) were analyzed using next-generation RNA sequencing.Furthermore, the data were validated using quantitative real-time PCR.Results:There were 534, 685 and 580 genes differentially expressed in 100 titer, moreover, 511, 485 and 531 differentially expressed genes (DEGs) were obtained from 10-2 titer for 66 h, 90 h and 114 h, respectively. These genes were mainly involved in functional categories including immune response, extracellular space, heparin binding, oxygen transport, extracellular region, cellular response to interleukin-4, MHC class II protein complex, antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, and pathways such as ribosome, ECM-receptor interaction, cell adhesion molecules, JAk-STAT signaling pathway, PPAR signaling pathway, neuroactive ligand-receptor interaction, phagosome.Conclusions: Different titers of DEV infection can stimulate different biological processes and signaling pathways in the spleen, and regulated the complex biological processes, metabolic and signaling pathways in the process of DEV infection.This transcriptome analysis of duck spleen infected with DEV in different time points is reported for the first time, it laid the foundation for further understanding of interactions between DEV and duck spleen tissue, molecular mechanisms of duck defend against DEV infection, and screening key functional genes.
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Project description:Hatchability is one of the important reproductive traits of poulty, however, molecular biological study related to hatchability of poultry is very limited. The magnum is where the egg white components are produced. During embryo development, egg white secreted by the magnum is gradually transferred into the amniotic fluid, and albumen finally migrates to the embryo. Egg white proteins are composed of ovalbumin, conalbumin, lysozyme, ovomucoid, riboflavin binding protein (RfBP), and other less abundant proteins. Mutation of ovalbumin and RfBP genes increases the mortality of embryos; therefore, egg white might be closely related to poultry hatchability. Tsaiya duck (Anas platyrhynchos) is the major egg-laying duck in Taiwan. In this study, gene expression profiling by cDNA microarray chip technology was performed using mRNA prepared from the magnum epithelium of Tsaiya ducks, and a number of differentially expressed transcripts were found. Keywords = Tsaiya duck (Anas platyrhynchos), magnum, hachability, cDNA microarray, transcriptional profiling.
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Project description:Hatchability is one of the important reproductive traits of poulty, however, molecular biological study related to hatchability of poultry is very limited. The magnum is where the egg white components are produced. During embryo development, egg white secreted by the magnum is gradually transferred into the amniotic fluid, and albumen finally migrates to the embryo. Egg white proteins are composed of ovalbumin, conalbumin, lysozyme, ovomucoid, riboflavin binding protein (RfBP), and other less abundant proteins. Mutation of ovalbumin and RfBP genes increases the mortality of embryos; therefore, egg white might be closely related to poultry hatchability. Tsaiya duck (Anas platyrhynchos) is the major egg-laying duck in Taiwan. In this study, gene expression profiling by cDNA microarray chip technology was performed using mRNA prepared from the magnum epithelium of Tsaiya ducks, and a number of differentially expressed transcripts were found. Keywords = Tsaiya duck (Anas platyrhynchos), magnum, hachability, cDNA microarray, transcriptional profiling. Analysis used low hachability RNA as control samples for comparison to the experimental samples taken from high hachability group. Total RNA was isolated by the RareRNA reagent (GenePure). The MicroMax direct labeling kit (PerkinElmer) was used to prepare the labeled cDNA and further process the hybridization on the arrays. Dye swap was design with four arrays. Arrays were scanned using a GenePix 4000B microarray scanner (Axon Instruments). GenePix Pro 4.1 software was then used to acquire the raw data. The data was analyzed by Avadis software (Strand Life Science).
2010-11-16 | E-GEOD-23100 | biostudies-arrayexpress