Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomics-based molecular epidemiology of human clinical and feedlot cattle C. jejuni isolates in Alberta, Canada

ABSTRACT: Oligonucleotide DNA microarrays were used as a platform to compare C. jejuni isolates from feedlot cattle and human clinical cases from Alberta. Comparative genomic hybridization (CGH) analysis was performed on 87 isolates (46 bovine, 41 human) obtained within the same geographical regions and time frame. In addition, We also performed gene association analysis to determine if any genes may be differentially distributed between human and cattle sources or between clusters dominated by either human or cattle isolates (“human enriched” vs “cattle enriched”). Keywords: Comparative Genomic Hybridization; Genomic epidemiology; Gene-association study

ORGANISM(S): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 Campylobacter jejuni

PROVIDER: GSE13228 | GEO | 2008/10/17

SECONDARY ACCESSION(S): PRJNA109463

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genomics-based molecular epidemiology of human clinical and feedlot cattle C. jejuni isolates in Alberta, Canada

Project description:Oligonucleotide DNA microarrays were used as a platform to compare C. jejuni isolates from feedlot cattle and human clinical cases from Alberta. Comparative genomic hybridization (CGH) analysis was performed on 87 isolates (46 bovine, 41 human) obtained within the same geographical regions and time frame. In addition, We also performed gene association analysis to determine if any genes may be differentially distributed between human and cattle sources or between clusters dominated by either human or cattle isolates (âhuman enrichedâ vs âcattle enrichedâ). Keywords: Comparative Genomic Hybridization; Genomic epidemiology; Gene-association study Data from 119 microarrays is included in the dataset, representing the 89 bacterial strains analyzed (87 field isolates, 2 control laboratory strains). Replicate arrays for 20 of the 87 field isolates were included in the dataset, as well as 5 replicates for each of the 2 laboratory controls. An array representing 1546 ORFs from strain NCTC 11168 was used in CGH experiments. CGH was performed by comparing signal from each Tester field isolate analyzed vs. signal from the Control strain NCTC 11168. Values represent mean of triplicate spots.

2010-05-18 | E-GEOD-13228 | biostudies-arrayexpress

Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle

Project description:Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the well-being and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. Therefore, this study utilized multi-omics data (genomics, transcriptomics, and metabolomics) analyses to study the associations between genome, transcriptome, metabolome, and BRD phenotype of feedlot crossbred cattle. The findings may be useful for the development of genomic selection strategies for BRD susceptibility, and for the development of new diagnostic and therapeutic tools.

2023-01-11 | GSE217317 | GEO

Comparative Genomic Hybridization of E. coli and Shigella species to determine the relatedness of isolates from Neobladders

Project description:Using comparative genomic hybridization we examined the genome content of 30 isolates of E. coli and Shigella to determine the relative location of E. coli isolates from the human neobladder

2011-07-25 | GSE27326 | GEO

Comparative genomic hybridizations of Mycobacterium avium isolates obtained from multiple host species

Project description:A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species. DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10. ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA. Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray. Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes. One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18. Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements. Keywords: Comparative genomic hybridization

2007-04-27 | GSE7622 | GEO

The nasopharyngeal microbiota of cattle with bovine respiratory disease

Project description:The nasopharyngeal microbiota of healthy cattle vs. cattle diagnosed with BRD in a commercial feedlot setting was compared using a high-density 16S rRNA microarray (Phylochip). Nasopharyngeal samples were taken from both groups of animals (n=5) at feedlot entry (day 0) and >60 days later.

2015-06-21 | E-MTAB-3430 | biostudies-arrayexpress

Genotyping of Coxiella burnetii strains collection

Project description:Genotyping based on genomic comparative hybridization of different isolates of coxiella burnetii compared to NMI reference strain

2011-12-31 | GSE31543 | GEO

Comparative genomic hybridizations of Mycobacterium avium isolates obtained from multiple host species

2010-06-11 | E-GEOD-7622 | biostudies-arrayexpress

Genomic diversity of Escherichia isolates from diverse habitats

Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates

2012-08-30 | GSE39667 | GEO

Cattle Feedlot Watering Bowls Western Canada

Project description:Water samples from Cattle Feedlot Watering Bowls Western Canada

| PRJNA820789 | ENA

A transcriptome analyses of Longissimus dorsi muscle in Nguni cattle finished on different feedlot diets

Project description:Background: The Nguni is an indigenous Bos taurus Sanga breed which is primarily used in extensive commercial and communal farming systems in South Africa. The Nguni is a small framed early maturing breed not preferred for finishing under feedlot systems, as the large framed later maturing types are favoured for high lean meat yield. In this study we aim to investigate differentially expressed genes in Longissimus dorsi muscle of Nguni cattle fed diets differing in energy levels finished under commercial feedlot conditions. Results: Twenty Nguni and twenty Bonsmara were fed either a low (10.9 MJ ME/kg) or a high (12.00 MJ ME/kg) energy diet for 120 days. At slaughter, muscle samples were taken for RNA extraction and RNA-sequencing. A total of 2214 differentially expressed genes (DEG) were observed between the two breeds regardless of diet. For the low energy diets, 2244 DEG in the Nguni and the Bonsmara were significantly expressed, while a higher number of were differentially expression between the Nguni and Bonsmara on high energy diet (3154 DEG). A difference of 288 DEG were identified between the Nguni fed on the low and high energy diets. Most of the fat deposition genes were upregulated in the Bonsmara (ASIP, OXT, SNAI3, FOX01, PPARGC1A), with lower levels in the Nguni. Conclusion: Clear breed differences were found for the number and level of gene expression, while a larger variation in DEG were observed between the two diets within in the Bonsmara breed.

2018-09-07 | GSE119563 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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