Gene Expression Profiling of Tumor Samples

Purified total RNA for GEP was then amplified and fluorescently labeled using a One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies). Cy3-labeled cRNAs were hybridized to a SurePrint G3 Human Gene Expression 8 × 60K v2 Microarray (Agilent Technologies). A signature analysis based on the gene expression was performed using the expression ratio of the tumor and the corresponding normal tissue (T/N). The expression signature/score was calculated from the average of genes in unique gene sets corresponding to each individual signature (TP53 inactivation^{28 (link)}, chromosomal instability [CIN]^{49 (link)}).

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Imamura T., Ashida R., Ohshima K., Uesaka K., Sugiura T., Ohgi K., Yamada M., Otsuka S., Hatakeyama K., Nagashima T., Sugino T., Urakami K., Akiyama Y, & Yamaguchi K. (2023). Characterization of pancreatic cancer with ultra-low tumor mutational burden. Scientific Reports, 13, 4359.

Publication 2023

One-Color Low Input Quick Amp Labeling Kit SurePrint G3 Human Gene Expression 8 × 60K v2 Microarray

Chromosomal instability Crnas Gene Gene expression Human Microarray Normal tissue Tp53 Tumor

Corresponding Organization :

Other organizations : Shizuoka Cancer Center

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Gene expression signature/score calculated from the average of genes in unique gene sets corresponding to each individual signature (TP53 inactivation, chromosomal instability [CIN])

control variables

None explicitly mentioned

controls

Positive control: None mentioned
Negative control: None mentioned

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