Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Broiler responses to virulent and avirulent Clostridium perfringens

ABSTRACT: Purpose: Analyze gene expression during C. perfringens colonization in the chicken Transcriptomic profile of mRNA from C. perfrinegns from in vivo and in vitro conditions were determined in biological duplicates by RNA-Seq using Illumina HiSeq 2500 Comparison of gene expression through RNA sequencing of necrotic enteritis C. perfrinegns type A of in vivo (chicken loops) and in vitro (lab culture)

ORGANISM(S): Clostridium perfringens

SUBMITTER: Valeria Parreira

PROVIDER: E-GEOD-70701 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparative transcriptome analysis by RNAseq of Necrotic Enteritis Clostridium perfringens in ligated intestinal chicken loops and in vitro conditions.

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

Broiler responses to virulent and avirulent Clostridium perfringens

Project description:Purpose: Analyze gene expression during C. perfringens colonization in the chicken Transcriptomic profile of mRNA from C. perfrinegns from in vivo and in vitro conditions were determined in biological duplicates by RNA-Seq using Illumina HiSeq 2500

2015-10-30 | GSE70701 | GEO

Targeted Mass Spectrometry Analysis of Clostridium perfringens Toxins

Project description:Clostridium perfringens is an anaerobic, gram-positive, spore-forming bacterium spread throughout the environment. This bacterium is a common agent in the gastrointestinal tracts of healthy human beings and other mammals. Simultaneously, this agent is one of the most significant producers of toxins among all known bacteria. This expressive toxicity is due to the bacterium’s ability collectively to produce different protein toxins and/or enzymes with diverse modes of action. The present study uses currently developed targeted proteomic methods for the simultaneous detection of selected C. perfringens protein toxins. The method was applied in different kinds of environmental matrices and was used to analyze toxins production in a set of collection strains.

2019-03-25 | PXD012528 | Pride

TMT labeled Comparative Proteomic Analysis Reveals Active Immune Response during Clostridium perfringens type C Infected Piglet Diarrhea

Project description:We performed a TMT labeling-based quantitative spleen proteomic analysis of the control group (SC), tolerance group (SR) and susceptible group (SS) to identify the differentially expressed proteins (DEPs), and screened potential molecular markers of piglet spleen tissues in response to C. perfringens type C infection.

2022-05-20 | PXD030745 | Pride

C. perfringens 13 strain vs 13?cpe1786 erm strain

Project description:Transcriptional profiling of C. perfringens 13 strain compared with strain 13?cpe1786 erm after growth in minimal medium with 0.5 mM cystine. two-condition experiment, 13 vs 13?cpe1786 erm, 4 biological replicates for each condition

2010-10-01 | E-GEOD-19359 | biostudies-arrayexpress

Genome-wide transcriptomic analysis of duodenum in broilers infused with crude Clostridium perfringens toxin in situ

Project description:We use a genome wide transcriptomic approach to assess the effects of C. perfringens toxin infusion in the duodenum of broilers

2015-05-31 | E-MTAB-1028 | biostudies-arrayexpress

The transcriptional profile of deoxycholate-induced sporulation in Clostridium perfringens food poisoning isolate

Project description:Clostridium perfringens type A is a common source of food poisoning in humans. Vegetative cells sporulate in the small intestinal tract and produce a major pathogenic factor, C. perfringens enterotoxin (CPE) during sporulation. Although sporulation plays a critical role in the pathogenesis of food poisoning, the mechanisms to induce in vivo sporulation remain unclear. Bile salts had been identified to mediate sporulation, and we have confirmed deoxycholate (DCA)-induced sporulation in C. perfringens strain NCTC8239 co-cultured with human intestinal epithelial Caco-2 cells. In this study, we performed global transcriptome analysis of strain NCTC8239 to elucidate the mechanism to induce sporulation by DCA. From the 55 contigs of C. perfringens strain NCTC8239, 2778 coding sequences were extracted. We designed a DNA probe by utilizing eArray provided by Agilent Technologies. The custom 8Ã15K oligonucleotide array, containing 60 mer oligonucleotide probes for 2,778 genes in strain NCTC8239, 2 bacterial control genes: 16S rRNA and 23S rRNA, and 3 human control genes: beta-2-microglobulin, glucuronidase beta and 18S rRNA, were ordered to Agilent Technologies. Each probe was spotted in five-fold on each microarray. Each strain was run in triplicate or quadruplicate.

2016-03-13 | E-GEOD-69649 | biostudies-arrayexpress

VirR and RevR regulate many Clostridium perfringens genes in a reciprocal manner

Project description:We further characterize the VirSR and RevR regulatory networks by profiling the C. perfringens strain JIR325 and its isogenic virR and revR regulatory mutants using strand-specific RNA-seq. Two independent biological replicates were sequenced for each strain, generating more than 90 million sequence reads for each RNA-seq library (wild type, 97,289,148 reads; virR mutant, 116,505,992 reads and revR mutant, 131,811,486 reads). Using the edgeR analysis package, 223 genes in the virR mutant and 88 genes in the revR mutant were found to be differentially expressed. Comparative transcriptomic analysis revealed that VirR acts as a global negative regulator, whilst RevR acts as a global positive regulator. Therefore, about 88% of the differentially expressed genes were up-regulated in the virR mutant, whereas 75% of the differentially expressed genes were down-regulated in the revR mutant. Importantly, we identified 22 genes that were regulated by both VirR and RevR. Of these genes, 18 or 82%, which included the sporulation-specific spoIVA, sigG and sigF genes, were regulated positively and negatively by RevR and VirR, respectively. Furthermore, mapped RNA-seq reads visualized as a user plot showed that there were 97 previously unannotated transcripts in the intergenic regions. These transcripts may potentially encode novel genes or small RNA molecules. This study has identified genes, antisense transcripts, and transcripts within intergenic regions and on the native plasmid, which are controlled by the VirSR or RevR regulatory system. The knowledge obtained will enable a more thorough annotation of the C. perfringens genome. Comparative transcriptomic analysis on the virR and revR regulatory mutants, and the wild-type strain JIR325

2016-08-03 | E-GEOD-72137 | biostudies-arrayexpress

Transcriptional Profiling Analysis of Host response to Clostridium perfringens Infection in Broilers

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

Transcritptome of a revR deletion mutant during Clostridium perfringens exponential phase growth.

Project description:RevR is a putative orphan response regulator with a high degree of similarity to YycF from Bacilus subtilis and PhoB from Clostridium kluyveri. A revR deletion mutant of C. perfringens strain 13 was generated and the transcriptome analysed using microarrays. Total RNA was isolated from exponentially growing cells from the revR mutant and the wild-type control. Gene expression levels were compared between the revR mutant and wild-type strain 13

2011-01-17 | E-GEOD-26508 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data