RNA was extracted in a similar manner as described above. The RNA concentration was determined by spectroscopy using a Nanodrop (ThermoFisher, ND-8000). Amplification and labelling of total RNA were performed using the GeneChip® PICO Reagent Kit following the manufacturer’s protocol (ThermoFisher 2016, P/N 902790). Biotin-labeled target samples were hybridized to the Clariom™ GO Screen containing probes for 19,409 protein-coding genes. Target hybridization was processed on the GeneTitan® Instrument according to manufacturer’s instructions provided for Expression Array Plates (P/N 952361). Images were analyzed using the GeneChip® Command Console Software (GCC) (ThermoFisher). Microarray data were processed using the statistical computing R-program package limma (Version 3.42.0) and Bioconductor tools [57 (link)]. The gene expression values were normalized using Robust Multi-array Average (RMA) [58 (link)]. Individual probes were grouped into gene-specific probe sets based on Entrez Gene using the metadata package goscreenhuhsentrezg (version 25.0.0) [59 (link)].
Genechip command console software gcc
Manufactured by Thermo Fisher Scientific
GeneChip® Command Console Software (GCC) is a software application developed by Thermo Fisher Scientific. It is designed to control and manage Affymetrix GeneChip® microarray instruments. The software provides a user interface for instrument operation, data acquisition, and basic data analysis.
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2 protocols using genechip command console software gcc
1
Microarray Analysis of Gene Expression
2
FFPE RNA Extraction and Microarray Analysis
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RNA was extracted from one slice (10 µm) from the FFPE samples (Qiagen RNEasy FFPE kit). Amplification and labeling of total RNA were performed using the GeneChip® PICO Reagent Kit following the manufacturer’s protocol (ThermoFisher 2016, P/N 902,790). Biotin-labeled target samples were hybridized to the Affymetrix HT HG-U133+ PM Array. Target hybridization was processed on the GeneTitan® Instrument according to the manufacturer’s instructions provided for Expression Array Plates (P/N 702,933). Images were analyzed using the GeneChip® Command Console Software (GCC) (ThermoFisher).
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