3D-Gene® Mouse miRNA Oligo chip (ver.21)

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	Samples of CCl-induced liver tumors (a mixture of five independent large tumors), DEN-induced liver tumors (a mixture of five independent large tumors), CCl-induced cirrhotic liver tissues (non-tumorous tissues of livers harboring tumors, a mixture of five tissues from five mice), and control liver tissue (olive oil-treated; a mixture of two tissues from two mice) were analyzed and compared by one-color microarrays (3D-Gene Microarray; Toray, Tokyo, Japan).

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Samples of CCl-induced liver tumors (a mixture of five independent large tumors), DEN-induced liver tumors (a mixture of five independent large tumors), CCl-induced cirrhotic liver tissues (non-tumorous tissues of livers harboring tumors, a mixture of five tissues from five mice), and control liver tissue (olive oil-treated; a mixture of two tissues from two mice) were analyzed and compared by one-color microarrays (3D-Gene Microarray; Toray, Tokyo, Japan).

Publication protocol

cDNA microarray analysis
Total RNA was prepared from snap-frozen liver tissues using the RNeasy Mini Kit (Qiagen, Chatsworth, CA). Samples of CCl-induced liver tumors (a mixture of five independent large tumors), DEN-induced liver tumors (a mixture of five independent large tumors), CCl-induced cirrhotic liver tissues (non-tumorous tissues of livers harboring tumors, a mixture of five tissues from five mice), and control liver tissue (olive oil-treated; a mixture of two tissues from two mice) were analyzed and compared by one-color microarrays (3D-Gene Microarray; Toray, Tokyo, Japan). After background subtraction, the raw microarray data were normalized using a standard global normalization technique, and the signal intensities were calculated as the fold changes of expression values. The data of differentially expressed genes that were significantly changed (>4-fold, compared with control) were subjected to Z-score transformation and loaded in a centroid-linkage hierarchical clustering assay using a Pearson correlation (uncentered) similarity metric with Cluster 3.0. Then, the Java TreeView software () was applied to reveal the hierarchical gene groups among the four samples. The Z-score was cropped to −1.5 to +1.5 when generating a two-color heat map.

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