Ontology highlight
ABSTRACT:
PROVIDER: PRJEB43441 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5416080_1.fastq.gz | Fastqsanger.gz | |||
| ERR5416080_2.fastq.gz | Fastqsanger.gz | |||
| ERR5416120_1.fastq.gz | Fastqsanger.gz | |||
| ERR5416120_2.fastq.gz | Fastqsanger.gz | |||
| ERR5416081_1.fastq.gz | Fastqsanger.gz |
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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.
2011-10-03 | GSE25511 | GEO
Project description:Gene expression profiling of peripheral blood leukocytes in 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.
2012-03-01 | GSE31387 | GEO
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.
2011-10-02 | E-GEOD-25511 | biostudies-arrayexpress
Project description:The gut of chicken is mostly colonised with Campylobacter jejuni and with 100 fold less C. coli. The competitive ability of C. coli OR12 over C. jejuni OR1 has been examined in experimental broiler chickens following the observation that C. coli replaced an established C. jejuni intestinal colonisation within commercial chicken flocks reared outdoors (El-Shibiny, A., Connerton, P.L., Connerton, I.F., 2005. Enumeration and diversity of campylobacters and bacteriophages isolated during the rearing cycles of free-range and organic chickens. Applied Environmental Microbiology. 71, 1259-1266).
2015-09-15 | GSE17805 | GEO
Project description:Gene expression profiling of peripheral blood leukocytes in 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 blood collected 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. Peripheral blood leukocytes were isolated from whole blood for analysis.
2012-03-01 | E-GEOD-31387 | biostudies-arrayexpress
Project description:Purpose: This study is to more comprehensively understand the genome-wide host response to avian pathogen E. coli (APEC). Methods: Four-week-old male broiler chickens were infected with APEC O1 or given saline as a control. Bursas were collected at 1 and 5 days post-infection (dpi). Infected birds were classified based upon lesions in liver, pericardium and air sacs as having mild or severe pathology, representing resistant and susceptible phenotypes, respectively. Twenty-two individual bursa RNA libraries were sequenced, each yielding an average of 27 million single-end, 100-bp reads. Results: There were 2469 novel genes in a total of 16,603 detected. Large numbers of significantly differentially expressed (DE) genes were enriched in susceptible versus resistant birds and in susceptible versus non-infected birds at 5 dpi, as well as in 5 dpi versus 1 dpi susceptible birds. The DE genes represented signal transduction, immune response, and cell growth and death pathways. Conclusions: These data provide considerable insight into potential mechanisms of resistance to ExPEC infection, thus paving the way to develop strategies for ExPEC prevention and treatment, as well as enhancing innate resistance by genetic selection in animals.
2017-02-09 | GSE70334 | GEO
Project description:Purpose: This study is to more comprehensively understand the genome-wide host response to avian pathogen E. coli (APEC). Methods: Male broiler chicks were challenged with APEC (or mock-challenged as controls), and bone marrow was harvested at 1 and 5 days post-infection (dpi). Based upon necropsy-scored lesions on liver, pericardium, and air sacs, the challenged birds were assigned to mild or severe pathology categories, representing resistant and susceptible phenotypes, respectively. RNA sequence data were first analyzed using the R package EdgeR to identify differentially expressed genes.GO and pathway analysis using the R package GOseq identified many immune-related pathways. Results: RNA sequencing resulted in 11 to 40 million single-end raw reads of 100 bp per sample. After alignment, an average of 80 % of the reads, with 5 % representing multiple mapping, were mapped to the chicken reference transcriptome. Among these detected unique transcripts, there were 2,404 novel genes mainly distributed on chromosomes 1, 2, 4, 3, Z, 5 in decreasing number. Genes were detected as differentially expressed (DE) between treatments (susceptible, resistant, and mock-challenged) at a given time point, or DE between 1 and 5 dpi within the same treatment group. Compared to mock-challenged birds on 5 dpi, susceptible birds exhibited extensive enhancement of their T cell and B cell development, as well as innate and adaptive immune response. However, for the 1 dpi group, susceptible birds exhibited a decreased gene expression of T and B cell development. The differences between the two phenotypes, susceptible and resistant birds, at 5 dpi showed that susceptible birds had increased gene expression of B-cell development and adaptive immune response. Conclusions: This is the first report to our knowledge examining the role of bone marrow cells in responding to APEC infection in broilers. This transcriptome study provides insight and global overview into the response of genes involved in the earliest phases of the immune response to APEC infection. Our data indicate a dynamic interaction between the innate and adaptive immune responses to APEC infection in susceptible birds, providing flexibility and redundancy in the host’s induction of cytokines and chemokines. Additionally, B cell and T cell development are also extensively affected by APEC infection for susceptible birds, resulting in drastic host impairment in early response to infection. The findings of present study shed light on the underlying chicken immune modulation against APEC infection. Also, this study will build a solid foundation for identifying host genetic variation that may be manipulated to enhance resistance to infection and may be useful as colibacillosis control targets.
2017-02-09 | GSE67302 | GEO
Project description:Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection of pregnant females causes fetal death and increased piglet mortality, but there is substantial variation in the extent of reproductive pathology between individual dams. This study used RNA-sequencing to characterize the whole blood transcriptional response to PRRSV in pregnant gilts during the first week of infection, and attempted to identify gene expression signatures associated with a low or high level of fetal mortality at necropsy, 21 days post-inoculation. RNA-sequencing experiment compared whole blood gene expression in two groups of gilts: a low fetal mortality group (LFM) and a high fetal mortality (HFM) group (n=8 per group). Two sets of contrasts were perfromed. First, a time-course experiment in which gene expression at day 2 (D2) post-inoculation was compared to day 0 (D0-just prior to inoculation) and expression at day 6 post-inoculation was compared to D2. Second, a comparison of gene expression between LFM and HFM groups at each of the three time-points (D0, D2, and D6).
2016-05-17 | E-GEOD-75304 | biostudies-arrayexpress
Project description:Avian pathogenic Escherichia coli (APEC) is a subset of extraintestinal pathogenic E. coli that causes detrimental losses to the poultry industry. Vaccines to reduce APEC in chickens have been partially successful, but many lack protection against multiple serotypes of APEC. Recombinant attenuated Salmonella vaccine (RASV) strains have been used to induce immunity against Salmonella in production chickens and can be modified to deliver foreign antigens as well. This study evaluated the transcriptome of chicken spleens and assessed prevention of APEC infection following vaccination with RASV strains, including a RASV carrying an E. coli antigen. Four-day-old White Leghorn chicks were orally vaccinated with RASV c8025(pYA3337) carrying an empty plasmid, c8025(pYA4428) carrying genes for E. coli common pilus (ECP), a combination of RASVs c8025(pYA3337) and c8025(pYA4428), or PBS (unvaccinated). To assess the host response to vaccination, antibody titers were measured by ELISA and spleen samples (n = 5) were collected from combination vaccinated and unvaccinated groups of four-week-old chickens for RNA sequencing. Five-week old chickens were challenged via air sac with APEC strains APEC-O2 and c7122 (O78). Blood was obtained 24 hours post-challenge, heart, liver, lung, and spleen were collected 48 hours post-challenge for enumeration of E. coli, and gross colibacillosis lesions were scored at necropsy. Chickens vaccinated with RASV strains elicited anti-E. coli EcpA, as well as cross reactive anti-E. coli IutA and IroN IgY antibodies. IgA results. In some organs, bacterial loads and lesions scores were numerically reduced, but no significant differences were detected for vaccinated compared to unvaccinated chickens. Transcriptome results. This data indicates that RASVs could be used to stimulate the immune system and is an initial step toward developing improved therapeutics to combat APEC infections in chickens.
2018-07-10 | GSE101198 | GEO