Journal: PLoS Pathogens

Article Title: Genome-Wide Analysis of Germline Signaling Genes Regulating Longevity and Innate Immunity in the Nematode Pristionchus pacificus

doi: 10.1371/journal.ppat.1002864

Figure Lengend Snippet: In this schematic of microarrays comparisons, each experiment is represented by two parameters - the ablation status and the bacteria fed, while the double arrows show the samples co-hybridized on the same array. In the first experiment E1, 3,335 genes were differentially expressed when germline ablated animals fed on E. coli were compared against un-ablated animals also fed on E. coli . In second experiment, E2, only 244 genes were differentially expressed when ablated animals exposed to S. marcescens were compared against ablated animals exposed only to E. coli , thus indicating that effects of germline ablation are the major transcriptional component towards increased lifespan and pathogen resistance. We also compared these data to transcriptional response of wild-type P. pacificus worms exposed to S. marcescens (experiment E3, 552 genes, AS, RR, II and RJS, unpublished data). Using these data, we calculated the comparison E4 between ablated versus unablated animals, both fed on S. marcescens , and found 2,962 differentially expressed genes.

Article Snippet: We used our custom designed oligonucleotide microarrays manufactured by Agilent Technologies, which contain ∼93,000 unique probes for the ∼23,000 P. pacificus predicted genes (NCBI GEO accession GPL14372, see for design details of custom microarrays).

Techniques:

Journal: BMC Genomics

Article Title: Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

doi: 10.1186/s12864-015-2208-7

Figure Lengend Snippet: Agreement between qPCR and microarray data

Article Snippet: After initial screening, unique probes showing no cross-hybridisation potential were selected to produce an 8 × 15 K Agilent custom oligo-DNA microarray design format (Agilent Design ID = 038391), comprising 15,208 user defined features and 536 Agilent positive and negative controls.

Techniques: Microarray

Journal: BMC Genomics

Article Title: Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

doi: 10.1186/s12864-015-2208-7

Figure Lengend Snippet: Least-squares regression fit between microarray and qPCR data. The fit between microarray and qPCR non-normalised (non) and normalised (TEF) Log2FC (Fold Change) is shown in respect to the identity line (dashed) for the selected target genes of T. thynnus

Article Snippet: After initial screening, unique probes showing no cross-hybridisation potential were selected to produce an 8 × 15 K Agilent custom oligo-DNA microarray design format (Agilent Design ID = 038391), comprising 15,208 user defined features and 536 Agilent positive and negative controls.

Techniques: Microarray

Journal: BMC Genomics

Article Title: Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758)

doi: 10.1186/s12864-015-2208-7

Figure Lengend Snippet: Combined expression profiles of target genes belonging to six largest T. thynnus tissue clusters. The profiles were derived by combining qPCR and microarray data for specific genes using their respective percentile ranks. Nonparametric Kruskal-Wallis test was used to determine statistical significance of the differences between tissues. Letter codes denote statistical significance at p < 0.05

Article Snippet: After initial screening, unique probes showing no cross-hybridisation potential were selected to produce an 8 × 15 K Agilent custom oligo-DNA microarray design format (Agilent Design ID = 038391), comprising 15,208 user defined features and 536 Agilent positive and negative controls.

Techniques: Expressing, Derivative Assay, Microarray