Journal: Journal of Allergy

Article Title: How Can Microarrays Unlock Asthma?

doi: 10.1155/2012/241314

Figure Lengend Snippet: Overview of the production and use of expression microarrays. 3′ Expression arrays use synthetically derived oligo probes with design based on mRNA Databases (RefSeq mRNAs, GenBank mRNAs, and ESTs from dbEST) or cDNA derived from bacterial libraries (see ). Sample mRNA can be labeled using two methods (a) Cy3/Cy5 labeling: sample mRNA is reverse transcribed into cDNA and Cy3 is added to one sample and Cy5 to another. Both labeled samples are hybridized to the same microarray. (b) 3′ IVT array: sample mRNA is reverse transcribed to cDNA using oligo(dT) primers, to provide a template for transcription. Using biotin-conjugated nucleotides, the template cDNA is then converted to amplified RNA (aRNA). The biotin-labeled aRNA samples are then fragmented and hybridized onto 3′ expression arrays. A biotin binding fluorescent stain is added to the microarray after hybridization. (c) Affymetrix HuExon 1.0 ST: sample mRNA is reverse transcribed to cDNA using random primers, to provide a template for transcription. The resulting RNA is then reverse transcribed in the presence of dUTPs which are incorporated occasionally into the cDNA sequence instead of dTTP. An enzyme is then used to cleave the cDNA at the site of dUTP incorporation and fragments are terminally labeled before hybridization onto the array. The microarray is then washed and stained after hybridization.

Article Snippet: In an attempt to identify the role of IL13 and its isotypes in the pathogenesis of allergic asthma, Syed et al. looked at the effect of IL13 and IL13R130Q on ASM using an expression microarray containing 8159 human gene cDNA clones from Research Genetics (IMAGE consortium, Huntsville, AL), Incyte Genomics (Santa Clara, CA) [ ].

Techniques: Expressing, Derivative Assay, Labeling, Reverse Transcription, Microarray, Amplification, Binding Assay, Staining, Hybridization, Sequencing

Journal: Journal of Allergy

Article Title: How Can Microarrays Unlock Asthma?

doi: 10.1155/2012/241314

Figure Lengend Snippet: The GEO accession number for microarray studies conducted on asthma.

Article Snippet: In an attempt to identify the role of IL13 and its isotypes in the pathogenesis of allergic asthma, Syed et al. looked at the effect of IL13 and IL13R130Q on ASM using an expression microarray containing 8159 human gene cDNA clones from Research Genetics (IMAGE consortium, Huntsville, AL), Incyte Genomics (Santa Clara, CA) [ ].

Techniques: Microarray, Gene Expression, Clone Assay, Expressing, Virus, Infection, Functional Assay, Sequencing, Synthesized, Comparison

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Linking toxicity and adaptive responses across the transcriptome, proteome, and phenotype of Chlamydomonas reinhardtii exposed to silver

doi: 10.1073/pnas.1319388111

Figure Lengend Snippet: Uptake and transport of silver in C. reinhardtii. Intracellular concentrations of silver (A) on exposure to 100 and 200 nM, and (Inset) to 500-nM exposure. No intracellular silver was quantifiable in C. reinhardtii exposed to 10 nM silver and is therefore not shown in the graph. Heat map of Cu transporters (B) in C. reinhardtii exposed to silver for varying durations with each box representing a protein at the transcriptome and proteome level, green being down-regulated and red up-regulated. The SD is shown in the figures. Atx1, antioxidant 1, copper chaperone; Cox2A, subunit 2A of cytochrome oxidase; Ctr1 and -3, copper transporter 1 and 3; Fox1, Ferroxidase; Pcy1, Plastocyanin. For the molecular responses, algae exposed to 500 nM Ag+ were not analyzed (see Methods).

Article Snippet: A C. reinhardtii whole-genome gene-expression microarray (Genotypic Technology) was designed using the JGI V4 Chlamydomonas best-transcripts database.

Techniques: Algae

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Linking toxicity and adaptive responses across the transcriptome, proteome, and phenotype of Chlamydomonas reinhardtii exposed to silver

doi: 10.1073/pnas.1319388111

Figure Lengend Snippet: Regulation of functional pathways in C. reinhardtii at physiological (A, C, E, G) and molecular (B, D, F, H) levels. Photosynthesis (A, B); lipid peroxidation compared with the control (C) and oxidative stress response (D); growth (E, F); ATP content (G) and synthesis (H). In the heat maps each square represents a protein, with green being down-regulated and red up-regulated. For the molecular responses, algae exposed to 500 nM Ag+ were not analyzed (see Methods).

Article Snippet: A C. reinhardtii whole-genome gene-expression microarray (Genotypic Technology) was designed using the JGI V4 Chlamydomonas best-transcripts database.

Techniques: Functional Assay, Control, Algae

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Linking toxicity and adaptive responses across the transcriptome, proteome, and phenotype of Chlamydomonas reinhardtii exposed to silver

doi: 10.1073/pnas.1319388111

Figure Lengend Snippet: Molecular and physiological changes of lipid synthesis in C. reinhardtii exposed to silver for 1 h. Regulation of proteins (A) and lipid bodies containing precursors of lipids stained green with Nile red (B). The chloroplasts autoflourescence is seen as red. (Scale bars in B, 10 µm.) For the molecular responses, algae exposed to 500 nM Ag+ were not analyzed (see Methods).

Article Snippet: A C. reinhardtii whole-genome gene-expression microarray (Genotypic Technology) was designed using the JGI V4 Chlamydomonas best-transcripts database.

Techniques: Staining, Algae

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Linking toxicity and adaptive responses across the transcriptome, proteome, and phenotype of Chlamydomonas reinhardtii exposed to silver

doi: 10.1073/pnas.1319388111

Figure Lengend Snippet: The toxicity and adaptive response pathways, as derived from linking transcriptome and proteome responses to physiological effects. (A) Schematic representation of biological pathways in C. reinhardtii affected by Ag+. (B) Schematic representation of the toxicity pathway. (C) Schematic representation of the adaptive-response pathway.

Article Snippet: A C. reinhardtii whole-genome gene-expression microarray (Genotypic Technology) was designed using the JGI V4 Chlamydomonas best-transcripts database.

Techniques: Derivative Assay