custom-designed oligonucleotide microarray genomedx v5  (GenomeDx Inc)

Journal: PLoS ONE

Article Title: Two Spx Regulators Modulate Stress Tolerance and Virulence in Streptococcus suis Serotype 2

doi: 10.1371/journal.pone.0108197

Figure Lengend Snippet: The relative transcriptional level of 10 selected genes determined by DNA microarray and qRT-PCR analyses were log 2 transformed, and the values were plotted against each other to evaluate their correlation. The genes analysed by qRT-PCR are listed in .

Article Snippet: DNA microarray analysis was performed using an Agilent custom-designed oligonucleotide microarray.

Techniques: Microarray, Quantitative RT-PCR, Transformation Assay

Journal: PLoS ONE

Article Title: Two Spx Regulators Modulate Stress Tolerance and Virulence in Streptococcus suis Serotype 2

doi: 10.1371/journal.pone.0108197

Figure Lengend Snippet: Expression ratios of genes involved in oxidative stress response and virulence in the mutant strains relative to the WT strain by microarray analysis a .

Article Snippet: DNA microarray analysis was performed using an Agilent custom-designed oligonucleotide microarray.

Techniques: Expressing, Mutagenesis, Microarray

Journal: Journal of Pediatric Genetics

Article Title: Mosaic Trisomy 16 Associated with Left Lung Agenesis, Abnormal Left Arm, and Right Pulmonary Artery Stenosis: Expanding the Phenotype and Review of the Literature

doi: 10.1055/s-0040-1721136

Figure Lengend Snippet: Array findings from prenatal single nucleotide polymorphism microarray on amniocytes (estimated 60% mosaicism). Image courtesy of LabCorp (Burlington, North Carolina, United States).

Article Snippet: The CMA on foreskin was performed on a custom designed oligonucleotide microarray (GenomeDx v5).

Techniques: Microarray

Journal: Journal of Pediatric Genetics

Article Title: Mosaic Trisomy 16 Associated with Left Lung Agenesis, Abnormal Left Arm, and Right Pulmonary Artery Stenosis: Expanding the Phenotype and Review of the Literature

doi: 10.1055/s-0040-1721136

Figure Lengend Snippet: Array findings from postnatal single nucleotide polymorphism microarray on foreskin tissue (estimated 25–40% mosaicism). Image courtesy of GeneDx (Gaithersburg, Maryland, United States).

Article Snippet: The CMA on foreskin was performed on a custom designed oligonucleotide microarray (GenomeDx v5).

Techniques: Microarray

Journal: PLoS ONE

Article Title: System Wide Analysis of the Evolution of Innate Immunity in the Nematode Model Species Caenorhabditis elegans and Pristionchus pacificus

doi: 10.1371/journal.pone.0044255

Figure Lengend Snippet: The rectangular boxes represent the entire transcriptomes of C. elegans and P. pacificus genes assayed on our microarrays, and their area of overlap represents the set of 6,126 1∶1 orthologs present on microarrays of both the nematodes. The ovals represent the fraction of differentially expressed genes in each of the subsets. For the 1∶1 orthologs, we assessed the significance of overlap between the genes differentially expressed in response to a given pathogen using a 2×2 Fisher's exact test. Differences or similarities in survival characteristics of the two nematodes when exposed to the same bacteria are reflected in their respective transcriptional responses. (A) On B. thuringiensis DB27, which is highly lethal to C. elegans but not to P. pacificus , only 23 genes are common between the respective expression profiles of the two nematodes, this overlap being statistically not significant. (B) Similarly, S. aureus is more lethal to C. elegans than P. pacificus , and the overlap between the corresponding expression profiles is limited to just 6 orthologs. Although this overlap is statistically significant (p-value = 0.0002), the extent of overlap is too small to be biologically significant. (C) S. marcescens is lethal to both the nematodes and the extent and significance overlap between the orthologs differentially expressed in the corresponding expression profiles is also relatively high (443 common orthologs, p-value = 7.71E–37). (D) On the pathogen X. nematophila , the observed overlap between the expression profiles in the two nematodes is even higher, with 2,093 orthologs regulated in both nematodes (p-value = 6.92E–134).

Article Snippet: For P. pacificus experiments, 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: Expressing