Heterologous Microarray Hybridization Between Vesicomyid Symbionts
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PROVIDER: PRJNA110047 | ENA |
REPOSITORIES: ENA
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Project description:The goal of this study was to use heterologous microarray hybridization to determine genomic content shared among different vesicomyid symbionts. These symbionts are closely related and can be thought of as different strains of bacteria, facilitating the use of heterologous microarray hybridization to determine genomic content. Keywords: comparative genomic hybridization
2008-11-28 | GSE13447 | GEO
Project description:The goal of this study was to use heterologous microarray hybridization to determine genomic content shared among different vesicomyid symbionts. These symbionts are closely related and can be thought of as different strains of bacteria, facilitating the use of heterologous microarray hybridization to determine genomic content. Keywords: comparative genomic hybridization Microarrays were built off the Ruthia magnifica genome and two replicate hybridizations to this organism were used as a baseline for comparisons. Genomic DNA from two other vesicomyid symbionts (Calyptogena kilmeri and C. pacifica symbionts) was also hybridized to the array with three biological replicates for each sample.
2010-05-15 | E-GEOD-13447 | biostudies-arrayexpress
Project description:The objective of this work was to determine the effectiveness of cross-hybridization of gDNA from five native soil nematodes to an Affymetrix Caenorhabditis elegans tiling array. Cross-hybridization experiments using C. briggsae, for which genome information is available, allowed hybridisation intensities to be correlated with known sequence differences. Initial analysis of data by conventional array-based Comparative Genomic Hybridization (aCGH) techniques at the chip level lead to misleading results due to an artefact from the combination of scaling, bandwidth smoothing, and differential GC content in exon and intron regions. To circumvent this artefact, individual probes were instead normalized and centered by adjusting for probe-specific thermodynamic binding affinity. However, cross-hybridization of C. briggsae DNA revealed that the resultant probe intensities alone were still uncorrelated to sequence similarity below 90% identity. Below 90% similarity, all probes hybridize uniformly poorly, and above 90% similarity the hybridization differences are not large enough to detect over background, therefore, no 'threshold' ratio of hybridization intensity was successful at identifying probes with similarity to the heterologous genome. In light of the observations described here, we suggest that the criteria for replication and verification of gene expression profiles generated from cross-species microarray hybridizations be more stringent than typically adopted for con-specific hybridizations.
2010-08-18 | GSE23667 | GEO
Project description:Mycorrhizal tissue was analyzed at five different time points after initial contact between the symbionts had occurred. The experimental design also included reference material grown axenically in parallel during the time course, with the purpose of detecting differential regulation of genes not related to the mycorrhizal interaction. For the mycorrhizal tissue, we sequentially and directly compared time points, including one loop-back hybridization, whereas the reference material was directly compared with mycorrhizal tissue within each time point. For the mycorrhizal material three biological replicates were included (Rep 1-3) whereas for the reference material only two were included (Rep 1 and 2), which equals 25 individual samples used. In total 40 separate labeling reactions and 20 microarray hybridizations were performed.
2005-08-30 | E-MEXP-180 | biostudies-arrayexpress
Project description:These experiments were designed to determine the usefulness of the spurge/cassava euphorbiaceae arrays for investigating gene expression in other euphorbs. Keywords: heterologous hybridization euphorbia
2007-08-24 | GSE8838 | GEO
Project description:We used two RNA samples that differed only by a set of three hemoglobin transcripts to compare microarray cross-hybridization between two target preparation protocols. We found widespread cross-hybridization using standard cRNA target but substantially less cross-hybridization using cDNA target. Keywords: protocol comparison
2006-09-08 | GSE4532 | GEO
Project description:Transcriptional profiling of colonic tumors compared to paired adjacent non-tumoral colonic tissue by two strategies. The first strategy is a conventional microarray assay, while the second strategy involves a previous Suppression Subtractive Hybridization (SSH) followed by a conventional microarray assay. We applied subtractive hybridization followed by microarray analysis to identify tumor-specific low-abundance transcripts. The goal was to determine differences in gene expression profile in tumor samples by both strategies.
2012-06-27 | GSE38939 | GEO
Project description:Transcriptional profiling of gastric tumors compared to paired adjacent non-tumoral gastric tissue by two strategies. The first strategy is a conventional microarray assay, while the second strategy involves a previous Suppression Subtractive Hybridization (SSH) followed by a conventional microarray assay. We applied subtractive hybridization followed by microarray analysis to identify tumor-specific low-abundance transcripts. The goal was to determine differences in gene expression profile in tumor samples by both strategies.
2012-06-27 | GSE38932 | GEO
Project description:Comparison of transcriptomes from bark, developing xylem and xylem of P. radiata saplings exposed to 0 or 1mg of Ethephon in lanolin for 1 or 8 weeks We developed an oligonucleotide microarray using sequences (mostly from Pinus taeda) from public sequence databases. These sequences were reconstituted into a non-redundant database by CAP3 assembly and used as templates for automated design of 60-mer oligonucleotide probes through eArray, Agilent’s online facility. The microarray slides, manufactured by Agilent, were used to monitor gene expression in an Ethephon-induction experiment. Ethephon was dispersed in lanolin paste and applied in a 3 cm band near the base of the stem of 2-year old Pinus radiata saplings. RNA was extracted from bark, cambial region, also known as “developing xylem”, and xylem tissues exposed for 1 or 8 weeks to Ethephon. The transcriptomes from these extracts were compared by hybridization onto the All-Pinus microarray slides. Statistically significant differentially expressed genes identified by limma (Linear Models for Microarray Data) were subsequently analysed by singular enrichment analysis through the Database for Annotation, Visualization and Integrated Discovery (DAVID) portal. Results revealed that bark, cambial region and xylem generate mostly mutually exclusive cohorts of genes and Gene Ontology (GO) classes. Ethephon induction led to the upregulation of xylem genes related to the metabolism of phenylpropanoids and flavonoids and to defence responses, specifically, fungal/insect attack and oxidative stress. Independent validation of the microarray data for five genes was obtained by quantitative RT-PCR. The results are also interpreted in reference to gross and microscopic morphological changes. These results confirm the utility of the All-Pinus microarray for transcriptomic research in P. radiata.
2012-11-15 | GSE42300 | GEO
Project description:Host-microbe interactions are virtually bidirectional, benefiting both the host and microbial sides. It is becoming increasingly recognized the influence of the microbe on many aspects of host physiology and diseases, but whether/how the host affects their symbionts is poorly characterized. Here, we reported that the host acts as a critical factor to shape the lifestyle of their symbionts in the Drosophila and bacteria model system. First, we observe that Drosophila larvae play a pivotal role in competing with pathogenic symbionts in the co-existing niche. More specifically, host larvae antagonize symbionts by deconstructing the surface slick, preventing outgrowth and antagonizing the pathogenicity of S. marcescens. Furthermore, Drosophila larvae cause the shift in the transcriptomic profile of S. marcescens, characterized with the upregulated expression of genes related to bacterial proliferation and growth and the downregulated expression of genes related to bacterial pathogenicity. More importantly, advances in bacterial single-cell RNA sequencing provide opportunities to reveal transcriptional variation, including toxic factors, across individual cells and a subpopulation clustering of isogenic bacterial populations. Finally, we found that AMPs from larvae recapitulated the response of S. marcescens to the presence of Drosophila larvae. Altogether, these findings provide an insight into the pivotal roles of the host in influencing the potential pathogens' lifecycle switching from commensalism to pathogenicity, opening the door to a better understanding of the ecological relationships between the host and microbe.
2024-01-17 | GSE232484 | GEO