Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1149910 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30304900.fastq.gz | Fastqsanger.gz | |||
| SRR30304901.fastq.gz | Fastqsanger.gz | |||
| SRR30304902.fastq.gz | Fastqsanger.gz | |||
| SRR30304903.fastq.gz | Fastqsanger.gz | |||
| SRR30304904.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Analyze gene expression of necrotic enteritis C. perfringens in intestinal chicken loops comparing with in vitro conditions
2016-10-07 | GSE79456 | GEO
Project description:Necrotic enteritis is a disease caused by Clostridium perfringens, which threatens poultry production in the absence of dietary antibiotics. A total number of 144 Ross broilers were reared in 12 pens with each hosting 12 birds. Each 6 pens of birds were fed medicated (bacitracin at 55 ppm) or non-medicated starter diets (Nutreco Canada Agresearch) immediately after the chicks were placed. At day 18, birds were challenged with C. perfringens (107 cfu per ml mixed with feed). Spleens were collected from 12 birds of each group at day 18 (before infection), 19, 20, and 22. A low-density chicken immune microarray was used to study gene expression profiling of host response to C. perfringens infection. Six biological replicates (2 birds per biological replicate) for each treatment group were labeled with either Cy5 or Cy3 with dye swap. A total of 24 arrays were used for this study. Gene signal intensity was globally normalized by LOWESS and expressed as log2 ratios. A mixed model including treatment, time, array, subgrid (random effect), dye, and all interactions among treatment and time was used to identify differentially expressed genes between post-infection vs. pre-infection, among post-infections, and between medication treatments, at the 5% significance level. The results indicated subtle medication effects on gene expression of these immune-related genes compared to bacterial infection effect. Our findings strongly suggest that both cell-mediated and antibody-mediated immune responses via MHC class I and II systems were actively involved in the host defense against C. perfringens infection in broilers. The unique cytokine signaling pathway and apoptosis cascade found in the study provide a new insight of molecular regulation of host immune response. Collectively, the findings of the present study will shed light on the molecular mechanisms underlying C. perfringens infection in broilers.
2009-03-01 | GSE13085 | GEO
Project description:Analysis of the blood proteome allows identification of proteins related to changes upon certain physiological conditions. The pathophysiology of necrotic enteritis (NE) has been extensively studied. While intestinal changes have been very well documented, data addressing NE-induced alterations in the blood proteome are scant, although these might have merit in diagnostics. Considering recent technological advancements in proteomics and pressing need for tools to access gut health, the current study employs mass-spectrometry (MS) proteomics to identify biomarkers for gastrointestinal health of broilers chickens. Untargeted proteomics investigation was conducted on chicken blood plasma in animals under NE challenge. Two MS-strategies were used for analysis: DDA (Data Dependent Acquisition) and DIA (Data Independent Acquisition). DIA showed superior completeness and quantification of the acquired data, despite high degree of agreement in identification and quantification between both approaches. Identified differentially expressed proteins shared by DDA and DIA represent responses of animals to infection and may serve as potential biomarkers. Experimental validation through ELISA immunoassays for selected regulated proteins confirmed medium-to-high levels of inter-protein correlation, along with positive correlation between the methods. Functional analysis showed enhanced defense, immune, and acute phase responses, alongside reduced signaling, regulatory, and cell adhesion activities in infected animals.
2025-05-07 | PXD061607 | Pride
Project description:Analysis of the blood proteome allows identification of proteins related to changes upon certain physiological conditions. The pathophysiology of necrotic enteritis (NE) has been extensively studied. While intestinal changes have been very well documented, data addressing NE-induced alterations in the blood proteome are scant, although these might have merit in diagnostics. Considering recent technological advancements in proteomics and pressing need for tools to access gut health, the current study employs mass-spectrometry (MS) proteomics to identify biomarkers for gastrointestinal health of broilers chickens. Untargeted proteomics investigation was conducted on chicken blood plasma in animals under NE challenge. Two MS-strategies were used for analysis: DDA (Data Dependent Acquisition) and DIA (Data Independent Acquisition). DIA showed superior completeness and quantification of the acquired data, despite high degree of agreement in identification and quantification between both approaches. Identified differentially expressed proteins shared by DDA and DIA represent responses of animals to infection and may serve as potential biomarkers. Experimental validation through ELISA immunoassays for selected regulated proteins confirmed medium-to-high levels of inter-protein correlation, along with positive correlation between the methods. Functional analysis showed enhanced defense, immune, and acute phase responses, alongside reduced signaling, regulatory, and cell adhesion activities in infected animals.
2025-05-13 | PXD050473 | Pride
Project description:Analysis of the blood proteome allows identification of proteins related to changes upon certain physiological conditions. The pathophysiology of necrotic enteritis (NE) has been extensively studied. While intestinal changes have been very well documented, data addressing NE-induced alterations in the blood proteome are scant, although these might have merit in diagnostics. Considering recent technological advancements in proteomics and pressing need for tools to access gut health, the current study employs mass-spectrometry (MS) proteomics to identify biomarkers for gastrointestinal health of broilers chickens. Untargeted proteomics investigation was conducted on chicken blood plasma in animals under NE challenge. Two MS-strategies were used for analysis: DDA (Data Dependent Acquisition) and DIA (Data Independent Acquisition). DIA showed superior completeness and quantification of the acquired data, despite high degree of agreement in identification and quantification between both approaches. Identified differentially expressed proteins shared by DDA and DIA represent responses of animals to infection and may serve as potential biomarkers. Experimental validation through ELISA immunoassays for selected regulated proteins confirmed medium-to-high levels of inter-protein correlation, along with positive correlation between the methods. Functional analysis showed enhanced defense, immune, and acute phase responses, alongside reduced signaling, regulatory, and cell adhesion activities in infected animals.
2025-05-13 | PXD050461 | Pride
Project description:Necrotic enteritis is a disease caused by Clostridium perfringens, which threatens poultry production in the absence of dietary antibiotics. A total number of 144 Ross broilers were reared in 12 pens with each hosting 12 birds. Each 6 pens of birds were fed medicated (bacitracin at 55 ppm) or non-medicated starter diets (Nutreco Canada Agresearch) immediately after the chicks were placed. At day 18, birds were challenged with C. perfringens (107 cfu per ml mixed with feed). Spleens were collected from 12 birds of each group at day 18 (before infection), 19, 20, and 22. A low-density chicken immune microarray was used to study gene expression profiling of host response to C. perfringens infection. Six biological replicates (2 birds per biological replicate) for each treatment group were labeled with either Cy5 or Cy3 with dye swap. A total of 24 arrays were used for this study. Gene signal intensity was globally normalized by LOWESS and expressed as log2 ratios. A mixed model including treatment, time, array, subgrid (random effect), dye, and all interactions among treatment and time was used to identify differentially expressed genes between post-infection vs. pre-infection, among post-infections, and between medication treatments, at the 5% significance level. The results indicated subtle medication effects on gene expression of these immune-related genes compared to bacterial infection effect. Our findings strongly suggest that both cell-mediated and antibody-mediated immune responses via MHC class I and II systems were actively involved in the host defense against C. perfringens infection in broilers. The unique cytokine signaling pathway and apoptosis cascade found in the study provide a new insight of molecular regulation of host immune response. Collectively, the findings of the present study will shed light on the molecular mechanisms underlying C. perfringens infection in broilers. There were two groups: medicated and non-medicated. Spleen were collected to isolate total RNA for gene expression profiling.For the microarray study, two birds from each pen were pooled within each group. To account for any bias inherent to the fluorescent dyes, three of the six medicated replicates were labeled with Cy3 and the other three were labeled with Cy5 at each time point. The same design was applied for the non-medicated group. There were six hybridizations between medicated and non-medicated replicates at each time point. Twenty-three out of 24 arrays were used (data from one array were discarded due to poor quality).
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