Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1024573 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26339618_1.fastq.gz | Fastqsanger.gz | |||
| SRR26339618_2.fastq.gz | Fastqsanger.gz | |||
| SRR26339619_1.fastq.gz | Fastqsanger.gz | |||
| SRR26339619_2.fastq.gz | Fastqsanger.gz | |||
| SRR26339620_1.fastq.gz | Fastqsanger.gz |
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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.
2024-04-04 | PXD044325 | Pride
Project description:Gene expression profiling of clostridium perfringens infection in broilers on medicated and non-medicated diets using chicken 44k agilent microarray. To elucidate molecular and ceelular mechanisms of bacitracin effect on CP infection in chickens by microarray technology.
2009-09-01 | GSE14759 | GEO
Project description:Purpose: The purpose of this study is to clarify the response of Clostridium perfringens ATCC 13124 to host polysaccharide. Methods: Clostridium perfringens ATCC 13124 cells were cultured anaerobically in a medium containing Minimal medium-like condition Poor + medium, medium in which hyaluronic acid or mucin was added to Poor + medium. Total RNA was extracted from bacterial cells by the Hot-Phenol method. Samples for RNA-seq were prepared according to the Illmina protocol available from the manufacturer. Array leads passed through quality filters were analyzed at the transcript isoform level using bowtie v 1.1.2. Results: Using the optimized data analysis workflow, we mapped about 50 million sequence leads per sample to the whole genome of Clostridium perfringens ATCC 13124. In addition, 2735 transcripts in C. perfringens ATCC 13124 were identified using a Bowtie aligner. Lead counts per genome were extracted from known gene annotations using the HTSeq program.
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Project description:Gene expression profiling of male broiler chickens exposed to APEC O1. Comparisons were made between Day 1 and Day 5 of all treatment groups, between differences in pathology and effect of vaccine on spleen gene expression. The goal was to determine expression differences that could convey genetic resistance to APEC O1. Chickens were either challenged or non-challenged with APEC, vaccinated or non-vaccinated, with spleens harvested 1 or 5 days post challenge. The non-vaccinated, challenged group was further subdivided into mild and severe pathologay based on internal lesion scores. This created 10 groups, done in 4 replicates. The non-vaccinated, non-challenged, day 1 group was used as the reference for all other samples.
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Project description:In the two F8 advanced crosses of broiler by Leghorn and broiler by Fayoumi, birds at day 1 were challenged with Salmonella enteritidis (SE). Spleen were collected at day 7 and 8. SE bacterial load in spleen were measured. Based on the bacterial load, birds were divided into high and low SE load groups. Keywords: Salmonella enteritidis challenge
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Project description:Purpose: RNA-Seq has become a powerful tool for investigating transcriptional profiles in gene expression analysis, which would help to reveal the molecular mechanism of Clostridium perfringens type C infecting the piglets. In this study, we analyzed the transcriptome profiles of the spleen of piglets caused by Clostridium perfringens type Cens type C. Methods: 30 normal 7-day-old piglets (Y x L), without infecting Clostridium perfringens type C, Escherichia coli and Salmonella, were selected as experimental subjects. 25 piglets were randomly selected as the experimental group, which were disposed once a day for 5 days. Each piglet was dosed with 1 ml of bouillon culture-medium inoculated Clostridium perfringens type C at 37℃ for 16h, which approximate to 1 x109 CFU per ml. Then, 5 piglets were randomly selected as the control group (SC), which were taken the equal volume medium for 5 days.Based on total diarrhea scores, 25 piglets were ranked from high to low. The top and last five piglet were considered as sensitive group (SS) and resistant group (SR), respectively. Finally, spleen were collected and sequenced for lncRNA and mRNA. Results: RNA libraries constructed from spleen of piglets caused by Clostridium perfringens type C were sequenced. A total of 1,450,292,484 clean reads were generated. Among them, 2056 novel lncRNA transcripts corresponding to 1561 lncRNA genes were identified, including 1811 intergenic lncRNAs and 245 anti-sense lncRNAs. The identified spleen lncRNAs shared some characteristics, such as fewer exons and shorter length, with the lncRNAs in other animal. Notably, in pairwise comparisons between the libraries of spleen tissue at the different group, a total of 247 lncRNA and 2170 mRNA were differentially expressed (P < 0.05). Function analyses indicated that these differentially expressed lncRNAs and mRNAs play roles in defensing Clostridium perfringens type C, which were enriched in immune-related biological processes, such as the antigen processing and presentation, TNF signaling pathway, NF-kappa B signaling pathway, B cell receptor signaling pathway and MAPK signaling pathway. Conclusions: This study provides the information of spleen-related lncRNAs in swine diarrhea with Clostridium perfringens type C. We also analyzed all lncRNA’s genomic feature and expression. Bioinformatic analysis indicates that some lncRNAs participated in important biological processes associated with defeasing Clostridium perfringens type C, such as antigen processing and presentation, the MHC protein complex and regulation of autophagy.
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Project description:Gene expression profiling of clostridium perfringens infection in broilers on medicated and non-medicated diets using chicken 44k agilent microarray. To elucidate molecular and ceelular mechanisms of bacitracin effect on CP infection in chickens by microarray technology. A total number of 600 Ross broilers were reared in 12 pens with each hosting 50 birds. Each 6 pens of birds were fed bacitracin-medicated (55 ppm) or non-medicated starter diets immediately after the chicks were placed. At day 18, birds were challenged with CP. Spleens were collected from 12 birds of each group at day 18 (before infection), 19, 20, and 22. Total RNA was labeled by Cy3 or Cy5 with dye swap. Gene signal intensity was globally normalized by LOWESS and expressed on natural log scale. A mixed model including treatment, time, array (random effect), dye, and all interactions among treatment, time was used to identify differentially expressed genes between treatments, at the 1% significance level.
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