RNA-seq chicken
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB66500 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12094934_1.fastq.gz | Fastqsanger.gz | |||
| ERR12094934_2.fastq.gz | Fastqsanger.gz | |||
| ERR12094935_1.fastq.gz | Fastqsanger.gz | |||
| ERR12094935_2.fastq.gz | Fastqsanger.gz | |||
| ERR12094936_1.fastq.gz | Fastqsanger.gz |
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Project description:Introduction: Skeletal muscle satellite cells (MuSCs, or stem cells) play a crucial role in muscle development, maintenance, and regeneration, serving both hypertrophic support and regenerative myogenesis. Syndecans (SDCs) act as communication bridges within the muscle microenvironment, regulating interactions with extracellular matrix components, and contributing significantly to tissue repair and inflammation. Specifically, syndecan-4 (SDC4) is involved in muscle regeneration at multiple stages. Methods: This study delves into the emerging challenge of wooden breast (WB) myopathy and its connection to SDC4. Our hypothesis proposes that disruptions in MuSC dynamics through SDC4 contribute to the increased incidence of breast myopathies observed in growing broilers. To test our hypothesis, non-affected and affected broilers were systematically selected, and the characteristics of WB myopathy were studied both in vitro and in vivo. SDC4 overexpression in MuSCs and blocking peptides corresponding to the SDC4 ectodomain were used for investigation of the role of SDC4 in muscle development and its shedding levels. Results and Discussion: Examination in vivo of affected muscles revealed smaller fibers and changes in metabolic pathways. In vitro studies unveiled disrupted proliferation of MuSCs in WB myopathy, accompanied by downregulation of several muscle markers. Investigation of a potentially role of SDC4 in the pathogenesis of WB myopathy revealed a decreased tendency in SDC4 gene expression and increased shedding of its ectodomain. Moreover, we showed that SDC4 overexpression is linked to decreased proliferation in MuSCs and affected myogenesis. We detected the impairment proliferation of WB-affected MuSCs, revealing critical insights into the dysfunctional state of these cells in myopathy. Additionally, by treating MuSCs with blocking peptides derived from the SDC4 ectodomain, we identified altered proliferation. Taken together, this work contributes valuable knowledge on the molecular mechanisms underlying WB myopathy and role of SDC4 in this chicken myopathy.
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Project description:Wooden Breast (WB) is a novel myopathy affecting the pectoralis major muscle of modern broiler chickens. We selected pectoralis fillet samples, a normal(healthy) fillet and a WB fillet.
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Project description:Satellite cell dynamics is impaired in chicken Wooden Breast myopathy via altered Syndecan-4 function
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Project description:Male Ross 308 broiler chickens (Gallus Gallus) were raised with ad libitum access to a pelleted wheat/maize diet from the 10th day of age. Breast muscle was acquired from the chickens at 36 days post-hatching. The degree of wooden breast (non-affected, moderately affected and affected) were first sorted by palpation of individual chickens, followed by classification using near-infrared (NIR) spectroscopy of breast filet and histology of specimen. Samples were grouped into three categories: affected, moderately affected and non-affected according to WB myopathy based on the connective tissue content (fibrotic signs). For the shotgun proteomics analysis, salt soluble proteins were extracted from breast filet. Twelve biological replicates of each group were included in the analysis. The proteins were reduced and alkylated prior to digestion with Trypsin/Lys-C. And peptides were analyzed by Dionex Ultimate 3000 UHPLC (Thermo Scientific) coupled to a Q-Exactive hybrid quadrupole Orbitrap mass spectrometer (Thermo Scientific).
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Project description:This experiment is contains chicken organism part samples and strand-specific RNA-seq data from experiment E-GEOD-41637 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41637/), which aimed at assessing tissue-specific transcriptome variation across mammals, with chicken used as an outgroup in evolutionary analyses. Each organism part was sourced from three different animals as biological replicates. This data set was originally submitted to NCBI Gene Expression Omnibus under accession number GSE41637 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE41637) and later imported to ArrayExpress as E-GEOD-41637.
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Project description:Optimization of broiler chicken breast muscle protein accretion is key for the efficient production of poultry meat, whose demand is steadily increasing. In a context where antimicrobial growth promoters use is being restricted, it is important to find alternatives as well as to characterize the effect of immunological stress on broiler chicken growth. Despite of its importance, research on broiler chicken muscle protein dynamics has been mostly limited to the study of mixed protein turnover. The present study aims to characterize the effect of a bacterial challenge and the feed supplementation of a citrus and a cucumber extract on broiler chicken individual breast muscle proteins fractional synthesis rates (FSR) using a recently developed dynamic proteomics pipeline. 21 day-old broiler chickens were administered a single 2H2O dose before being culled at different timepoints. A total of 60 breast muscle protein extracts from five experimental groups (Unchallenged, Challenged, Control Diet, Diet 1 and Diet 2) were analyzed using a DDA proteomics approach. Proteomics data was filtered in order to reliably calculate multiple proteins FSR making use of a newly developed bioinformatics pipeline. Broiler breast muscle proteins FSR uniformly decreased following a bacterial challenge, this change was judged significant for 15 individual proteins, the two major functional clusters identified as well as for mixed breast muscle protein. Citrus or cucumber extract feed supplementation did not show any effect on the breast muscle protein FSR of immunologically challenged broilers. The present study has identified potential predictive markers of breast muscle growth and provided new information on broiler chicken breast muscle protein turnover which could be essential for improving the efficiency of broiler chicken meat production.
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