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