Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Camplyobacter jejuni isolates from humans and chickens

ABSTRACT: This experiment compares C.jejuni isolates from humans and chicken. The samples were collected during a Swedish outbreak. The chicken samples were collected from groceries from the same geographical reagions as the infected humans. The genotypes of the C.jejuni isolates were compared using three different methods.

ORGANISM(S): Campylobacter jejuni

SUBMITTER: Valtteri Wirta

PROVIDER: E-TABM-460 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Project description:Clostridium difficile is a gram-positive, spore-forming enteric anaerobe which can infect humans and a wide variety of animal species. Recently, the incidence and severity of human C. difficile infection has markedly increased. In this study, we evaluated the genomic content of 73 C. difficile strains isolated from humans, horses, cattle, and pigs by comparative genomic hybridization with microarrays containing coding sequences from C. difficile strains 630 and QCD-32g58. The sequenced genome of C. difficile strain 630 was used as a reference to define a candidate core genome of C. difficile and to explore correlations between host origins and genetic diversity. Approximately 16% of the genes in strain 630 were highly conserved among all strains, representing the core complement of functional genes defining C. difficile. Absent or divergent genes in the tested strains were distributed across the entire C. difficile 630 genome and across all the predicted functional categories. Interestingly, certain genes were conserved among strains from a specific host species, but divergent in isolates with other host origins. This information provides insight into the genomic changes which might contribute to host adaptation. Due to a high degree of divergence among C. difficile strains, a core gene list from this study offers the first step toward the construction of diagnostic arrays for C. difficile.investigated by determining changes in transcript profiles when aerobic steady-state cultures were depleted of air. Dye-swap experiments with genomic DNA of tested and reference strains 8383cy3.gpr- Cy3 – test, Cy5 – reference 8384cy3.gpr- Cy3 – test, Cy5 – reference 8384cy5.gpr- Cy3 – reference, Cy5 – test 8385cy3.gpr- Cy3 – test, Cy5 – reference 8385cy5.gpr- Cy3 – reference, Cy5 – test 8386cy3.gpr- Cy3 – test, Cy5 – reference 8525cy3.gpr- Cy3 – test, Cy5 – reference 8525cy5.gpr- Cy3 – reference, Cy5 – test 8527cy5.gpr- Cy3 – reference, Cy5 – test 8529cy5.gpr- Cy3 – reference, Cy5 – test 8531cy3.gpr- Cy3 – test, Cy5 – reference 8531cy5.gpr- Cy3 – reference, Cy5 – test 8533cy3.gpr- Cy3 – test, Cy5 – reference 8533cy5.gpr- Cy3 – reference, Cy5 – test 8596cy3.gpr- Cy3 – test, Cy5 – reference 8596cy5.gpr- Cy3 – reference, Cy5 – test 8694cy3.gpr- Cy3 – test, Cy5 – reference 8694cy5.gpr- Cy3 – reference, Cy5 – test 2 GPR files per Sample record except for 4 Sample records (GSM480414, GSM480417, GSM480419, and GSM480420) which have 1 GPR file each 4 GPR file for those Sample records are lost

Project description:Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign. There are 20 samples in total. These consist of 10 FAIRE-seq samples, specifically 6 haploid samples, S. cerevisiae strain UWOPS05_217_3 replicates 1 and 2, S. cerevisiae strain DBVPG1373 replicates 1 and 2, and S. paradoxus strain CBS432 replicates 1 and 2. There are also 4 diploid hybrid samples, hybrid between S. cerevisiae strain UWOPS05_217_3 and S. paradoxus strain CBS432 replicates 1 and 2, and the hybrid between S. cerevisiae strain DBVPG1373 and S. paradoxus strain CBS432 replicates 1 and 2. There are also RNA-seq samples for each of these 10 samples.

Project description:Chickens divergently selected for either high abdominal fat content (fat genotype) or low abdominal fat content (lean genotype) at SRA-INRA, France were used to profile abdominal adipose gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The fat line (FL) and lean line (LL) chickens are different in various phenotypic and metabolic measurements, including abdominal fatness, plasma glycemia and T3. The FL and LL chickens represent unique models for characterizing biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in abdominal adipose during juvenile development using a balanced block hybridization design. Fluorescence intensities were normalized within array (without background subtraction), and between array (aquantile method) in LIMMA package R [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3] producing M-values (log-2 expression ratios) and A-values (average log-2 expression values). Normalized values were analyzed using a two factor ANOVA model. A total of 1,020 differentially expressed functional genes were identified (FDR<0.05). Genes were determined to have a significant effect of age (422), genotype (344), or an age by genotype interaction (254). The differentially expressed genes include metabolic enzymes, acute phase proteins, growth factors, coagulation factors, immune factors and transcription factors involved in various pathways. Several of the functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the FL and LL lines. Keywords: Divergently selected chickens, fatness, transcriptional profiling, differentially expressed genes A balanced block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (FL or LL) at six different ages (1, 3, 5, 7, 9 and 11 wk).

Project description:Campylobacter, a major foodborne pathogen, is increasingly resistant to macrolide antibibotics. Previous findings suggeted that development of macrolide resistance in campylobacter requires a multi-step process, but the molecular mechanisms involved in the process are not known. In our study, multiple series of macrolide-resistant C. jejuni mutants were selected in vitro by stepwise exposure of C. jejuni NCTC11168 to increasing concentrations of erythromycin and tylosin. A set of the selected resistance were subjected to microarray and the the global transcriptional profile was analyzed. In this sery, DNA microarray was used to compare the gene expression profiles of macrolide resistant strains (68E1, 68E8 and 68E64) with its parent wild-type strain NCTC11168. The assay identified a small number of genes that showed significant changes (q-value<0.1) in expression in the low-level macrolide resistant strain 68E1, while a large number of gene showing significant changes in intermedia-level resistant stran 68E8 and high-level resistant strain 68 E64. The up-regulated genes in the resistant strains are involved in miscellaneous periplasmic proteins, efflux protienand putative aminotransferase, while the majority of the down-regulated genes are involved in electron transport,lipoprotein, heat shock protein and unknown function proteins. These findings suggest that there is not much change in low-level macrolide resistant C. jejuni strain. The over-expression of efflux pump and periplasmic protein was involved in the development of resistance to macrolide in C. jejuni. Keywords: macrolide resistant C. jejuni selected from NCTC 11168 step-wise selection. The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni. Four hybridizations were performed each with independently extracted samples of either macrolide susceptible C. jejuni NCTC11168 cDNA samples or macrolide resistant C.jejuni cDNA samples. A dye swap was utilized to help minimize dye dependent bias. Thus, there were four biological replicates of each sample.

Project description:CpG DNA interacts with TLR9 to stimulate a broadly protective innate immune response. This study uses bioinformatic network analysis of microarray data to identify the genes and regulatory networks triggered by CpG ODN. CpG treatment induced significant gene up-regulation (p < 0.00001) in the spleen within 30 min, peaking with the activation of >500 genes at 3 hr, and declining progressively thereafter. There were reproducible changes in the pattern of gene expression over time. This was mediated by a small group of “major inducers” (IL1A, IL1B, TNF, IFNG) whose activity was modulated by several “minor inducers” (NFKB1, IL6, IL15, IL18, STAT1, STAT2). The subsequent decline in gene activation was mediated by “suppressors” (MYC, IL1RN, SOCS1, SOCS3, NFKBIA, IL10, FOS) that actively down-regulated gene expression and targeted both major and minor inducers. Thus, the regulation of TLR9 dependent gene activation involves multiple waves of stimulation mediated by a small number of “major” and “minor” inducers followed by the active inhibition of gene expression by “suppressors”. Keywords: time series design Endotoxin-free phosphorothioate ODN were synthesized at the CBER core facility (FDA, Bethesda, MD) as previously described. Mice were injected intraperitoneal (i.p.) with 400 ìg of an equimolar mixture of CpG ODNs 1555 (GCTAGACGTTAGCGT) and 1466 (TCAACGTTGA) or control ODNs 1612 (GCTAGATGTTAGCGT) and 1471 (TCAAGCTTGA). Spleens were surgically removed from mice under sterile conditions after 0.5, 1, 3, 9, 24 hr, and/or 72 hr, diced, and stored at -800 C in RNAlater (Qiagen, Valencia, CA). Data from 4 independent experiments/time point and 4-6 untreated controls were used for all statistical analyses. Reproducibility was established by comparing gene expression profiles among similarly treated mice from independent experiments in mAdb (referenced above). Expression analyses were performed using BRB ArrayTools (Biometric Research Branch, NCI). Data were background corrected, flagged values were removed, spots in which both signals were <100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes (Yang et al., 2002). Analysis was restricted to genes present on >70% of the arrays after filtering. The gene expression profile of all treatment groups was compared to that of the control groups.