Genome-wide mRNA Expression Analysis

mRNA of RKOp53wt and RKOp53KO cells was isolated with an RNeasy Mini Kit from Qiagen (Hilden, Germany) according to the manufacturer’s instructions. Quality and integrity of mRNA was checked on the Agilent 2100 Bioanalyzer, and only samples with RIN values >9 were included for microarray analysis. Whole genome oligonucleotide-based gene expression microarray analysis was performed using the 4 × 44 K microarray format as described previously [48 (link)]. Dual-color experiments were performed using the Quick Amp Labelling Kit according to the instructions provided (Agilent, Santa Clara, CA, USA). Slides were scanned on a G2505B Micro Array Scanner (Agilent). Feature Extraction and data analysis were carried out using the Feature Extraction and GeneSpring software (both Agilent).

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Dinhof C., Pirker C., Kroiss P., Kirchhofer D., Gabler L., Gojo J., Lötsch-Gojo D., Stojanovic M., Timelthaler G., Ferk F., Knasmüller S., Reisecker J., Spiegl-Kreinecker S., Birner P., Preusser M, & Berger W. (2020). p53 Loss Mediates Hypersensitivity to ETS Transcription Factor Inhibition Based on PARylation-Mediated Cell Death Induction. Cancers, 12(11), 3205.

Publication 2020

RNeasy Mini Kit Quick Amp Labelling Kit G2505B Micro Array Scanner Feature Extraction

Cells Gene expression microarray analysis Genome Microarray Mrna Oligonucleotide

Corresponding Organization : Comprehensive Cancer Center Vienna

Other organizations : Kepler Universitätsklinikum

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Variable analysis

independent variables

RKOp53wt cells
RKOp53KO cells

dependent variables

MRNA expression profile

control variables

MRNA isolation using RNeasy Mini Kit from Qiagen
MRNA quality and integrity checked on Agilent 2100 Bioanalyzer
Whole genome oligonucleotide-based gene expression microarray analysis using 4 × 44 K microarray format
Dual-color experiments performed using Quick Amp Labelling Kit
Slides scanned on G2505B Micro Array Scanner (Agilent)
Feature extraction and data analysis using Feature Extraction and GeneSpring software

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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