Total RNA of KYSE150 cells and CAFs was extracted using mirVana™ RNA isolation kit (Invitrogen, Cat# AM1561). Obtained RNA (0.5 μg) was used for synthesis of Cyanine-3 (Cy3)-labeled cRNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent). Then RNAeasy column was used for purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 spectrophotometer. Microarray was conducted using Agilent SurePrint G3 Human Gene Expression v3 (8 × 60 K). The hybridized arrays were scanned with the Agilent Scanner G2505C microarray scanner, and the data was extracted and normalized using Agilent Feature Extraction software (version 10.7.1.1). Further data analysis was performed using Agilent GeneSpring software (version 13.1). The accession number of microarray data in the GEO database was GSE194414.
Sureprint g3 human gene expression v3 8 60 k
Manufactured by Agilent Technologies
Sourced in United States
The SurePrint G3 Human Gene Expression v3 (8 × 60 K) is a microarray designed for comprehensive gene expression analysis of the human genome. It features 60,000 probes covering the majority of human genes.
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Lab products found in correlation
One color low rna input linear amplification plus kit, by Agilent Technologies (1 mentions)
Mirvana rna isolation kit, by Thermo Fisher Scientific (1 mentions)
Rnaeasy column, by Qiagen (1 mentions)
Feature extraction software, by Agilent Technologies (1 mentions)
Agilent scanner g2505c, by Agilent Technologies (1 mentions)
2 protocols using sureprint g3 human gene expression v3 8 60 k
1
Transcriptomic Profiling of KYSE150 Cells and CAFs
2
Ovarian Cancer Transcriptomic Analysis
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3 normal ovarian epithelial tissue and 3 benign epithelial ovarian tumor tissue were used for RNA isolation through AMBION kit (Invitrogen, USA). After passing quality inspection, the total RNA was transcribed into double stranded cDNA, synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray (Agilent SurePrint G3 Human Gene Expression v3, 8*60 K, Design ID: 072363) and scanned by the Agilent Scanner G2505C (Agilent Technologies, USA). The raw data was normalized using Extraction and GeneSpring. Differentially expressed genes were identified through fold change as well as P values calculated using Student’s-test. The threshold set for up- and down- regulated genes was a fold change ≥ 2.0 and a P value ≤ 0.01. The gene chip scanning was conducted in the laboratory of the OE Biotech Company (Shanghai, China).
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