Transcriptomic Analysis of Human Samples

Similar to previous studies^{18 (link)}, total RNA was extracted using a NucleoSpin® RNA Plus kit (Takara Bio, Shiga, Japan) according to the manufacturer’ s instructions. cDNA was synthesized using GeneChip® WT PLUS reagent kit (Thermo Fisher Scientific, Waltham, MA, USA) and hybridized to the array in Clariom^TM S human assay (Affymetrix, Santa Clara, CA, USA). The arrays were scanned and normalized with the Signal Space Transformation-Robust Multi-array Average algorithm using the Affymetrix GeneChip Command Console (Thermo Fisher Scientific). Differential gene expression analysis was performed using Transcriptome Analysis Console Software 4.0.2.15 (Thermo Fisher Scientific).

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Katayama Y., Yamada T., Tanimura K., Tokuda S., Morimoto K., Hirai S., Matsui Y., Nakamura R., Ishida M., Kawachi H., Yoneda K., Hosoya K., Tsuji T., Ozasa H., Yoshimura A., Iwasaku M., Kim Y.H., Horinaka M., Sakai T., Utsumi T., Shiotsu S., Takeda T., Katayama R, & Takayama K. (2023). Adaptive resistance to lorlatinib via EGFR signaling in ALK-rearranged lung cancer. NPJ Precision Oncology, 7, 12.

Publication 2023

NucleoSpin® RNA Plus kit GeneChip® WT PLUS reagent kit Affymetrix GeneChip Command Console Transcriptome Analysis Console Software 4.0.2.15

Assay Cdna Genechip Human Transcriptome analysis

Corresponding Organization :

Other organizations : Kyoto Prefectural University of Medicine, University of Occupational and Environmental Health Japan, Kyoto University, Kyoto first Red Cross hospital, Japanese Red Cross Society Kyoto Daini Hospital

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Variable analysis

independent variables

RNA extraction method
CDNA synthesis method
Microarray platform

dependent variables

Gene expression levels

control variables

Not explicitly mentioned

controls

Positive control: Not specified
Negative control: Not specified

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