Journal: International Journal of Chronic Obstructive Pulmonary Disease

Article Title: Identifying targets for COPD treatment through gene expression analyses

doi:

Figure Lengend Snippet: Summary of gene expression profiling studies involving human COPD/emphysema samples

Article Snippet: COPD GOLD2 vs. GOLD0 , Whole lung , Incyte Unigem high-density microarray (10,000 transcripts) SAGE (59,000 tags) , Apoptosis-related genes Inflammation-related genes Transcription factors (increased) Collagens (decreased) , Egr-1/Fos CTGF, CYR61, CX3CL1, TGFB1, and PDGFRA , .

Techniques: Expressing, Functional Assay, Microarray

Journal: Gene Expression

Article Title: Global Gene Expression Profiling of Dimethylnitrosamine-Induced Liver Fibrosis: From Pathological and Biochemical Data to Microarray Analysis

doi:

Figure Lengend Snippet: A schematic illustration of DMN-induced fibrosis in rats. (A) Each rat was either injected with DMN three times per week for 3 consecutive weeks (triangle) or injected with normal saline as a control under the same regime. Rats were weighed and sacrificed each week (starting on day 11, which are referred to as first week to sixth week). Blood samples were collected for biochemical assay (summary in Table 1) and livers were excised and weighed, followed by either fixing in formaldehyde for histopathology or isolation of RNA for microarray analysis. (B) The quantitative real-time PCR result for Tgfbl. The TaqMan® assays were conducted in triplicate for each sample, and a mean value was used for calculation of expression levels. To standardize the quantification of the target genes, 18S rRNA from each sample was quantified at the same time as the target genes.

Article Snippet: Secondly, Kim and his colleagues identified 556 chronic liver disease (CLD)-related genes, which included 273 HCC-associated gene signatures and 283 etiology-associated signatures; this involved a comparison of low-risk and high-risk CLD groups using an Incyte human cDNA microarray ( 26 ).

Techniques: Injection, Histopathology, Isolation, Microarray, Real-time Polymerase Chain Reaction, Expressing

Journal: Gene Expression

Article Title: Global Gene Expression Profiling of Dimethylnitrosamine-Induced Liver Fibrosis: From Pathological and Biochemical Data to Microarray Analysis

doi:

Figure Lengend Snippet: The 256 gene expression patterns of experimental samples. (A) Hierarchical clustering results of these gene expression patterns. The results are shown in a diagram format, in which rows represent individual transcripts and columns represent time course sample. The color in each cell reflected the expression level of the corresponding sample, relative to its mean expression level. The scale extends from fluorescence ratios of 0.25 to 4 relative to the mean level for all samples. (B) Gene ontology results of 256 genes. The plots of different category of these genes by gene ontology database (http://fatigo.bioinfo.cnif.es/). (C) The hierarchical clustering results of the three biology processes are: metabolism, cell growth and/or maintenance and response stimulus. These diagrams are formatted as rows representing individual transcripts and columns representing time course sample. The color in each cell reflects the expression level of the corresponding sample relative to its mean expression level and the scale extends from fluorescence ratios of 0.25 to 4 relative to the mean level for all samples. (D) The comparison of Timpl expression between the Q-RT-PCR results and microarray data. The TaqMan® assays were conducted in triplicate for each sample, and a mean value was used for calculation of expression levels (marked by the square). To standardize the quantification of the Timpl, 18S rRNA from each sample was quantified at the same time as the target gene and a log scale was used as indicated on the right side of plot. For the two Timpl transcripts, rc_AI169327_at and rc_AI169327_g_at (marked by circle and triangle), the expression levels of the microarray data were relative to the mean of all gene expression levels and the scale is indicated on the left side of plot. The Pearson correlation coefficients (r), which compared the Q-RT-PCR result and the microarray data of two Timpl transcripts (rc_AI169327_at and rc_AI169327_g_at), were 0.79 and 0.92, respectively. (E) Endogenous Spp1 protein expression pattern in DMN-induced rat liver samples. Rat liver samples were lysed and 50 itg protein lysates were subjected to immunoblot analysis with antibody against Spp1 and Actb. Spp1 was significantly overexpressed at the protein level after the fourth week of DMN treatment.

Article Snippet: Secondly, Kim and his colleagues identified 556 chronic liver disease (CLD)-related genes, which included 273 HCC-associated gene signatures and 283 etiology-associated signatures; this involved a comparison of low-risk and high-risk CLD groups using an Incyte human cDNA microarray ( 26 ).

Techniques: Expressing, Fluorescence, Reverse Transcription Polymerase Chain Reaction, Microarray, Western Blot

Journal: Gene Expression

Article Title: Global Gene Expression Profiling of Dimethylnitrosamine-Induced Liver Fibrosis: From Pathological and Biochemical Data to Microarray Analysis

doi:

Figure Lengend Snippet: SUMMARY OF MICROARRAY DATASETS COMPARISON

Article Snippet: Secondly, Kim and his colleagues identified 556 chronic liver disease (CLD)-related genes, which included 273 HCC-associated gene signatures and 283 etiology-associated signatures; this involved a comparison of low-risk and high-risk CLD groups using an Incyte human cDNA microarray ( 26 ).

Techniques: Microarray, Mouse Assay, Marker, Binding Assay, Translocation Assay

Journal: Gene Expression

Article Title: Global Gene Expression Profiling of Dimethylnitrosamine-Induced Liver Fibrosis: From Pathological and Biochemical Data to Microarray Analysis

doi:

Figure Lengend Snippet: THE GENE EXPRESSION PATTERNS OF FIBROSIS MARKERS BY QUANTITATIVE REAL-TIME PCR AND MICROARRAY DATA

Article Snippet: Secondly, Kim and his colleagues identified 556 chronic liver disease (CLD)-related genes, which included 273 HCC-associated gene signatures and 283 etiology-associated signatures; this involved a comparison of low-risk and high-risk CLD groups using an Incyte human cDNA microarray ( 26 ).

Techniques: Expressing, Real-time Polymerase Chain Reaction, Microarray, Reverse Transcription Polymerase Chain Reaction

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