RNA was isolated from pre-treatment tumor biopsy specimens as described previously 15 . Briefly, miRNA was extracted from pre-treatment biopsy specimens using mirVana miRNA Extraction Kit (Ambion). A NanoDrop Spectrophotometer (Thermal Scientific) was used to quantitate the specimens as well as assess the purity of the RNA. Additionally, the spectrum of each specimen was visually analyzed to ensure all profiled samples had a normal spectral profile. These samples were analyzed for miRNA expression using 3 separate platforms: TaqMan Human MicroRNA Card Set (v3.0) (Applied Biosystems), Fluidigm 48.48 Dynamic Array (Fluidigm), and Illumina Human MicroRNA expression beadchip (v2.0) (Illumina) per the manufacturer’s instructions. Our discovery cohort was assayed using TaqMan array, the model cohort was assayed using a Fluodigm array, and our validation cohort was examined using an Illumina array. This was done to ensure validity across multiple assay platforms. Each miRNA assay was tested in duplicate, and the mean Ct value was normalized to the averaged expression of spike-in miRNAs cel-39 and cel-54, and then subjected to analysis using the 2−ΔΔCt method 16 (link). For the Taqman array, miRNAs detected in less than 20% of samples were excluded from analysis.
Human microrna expression beadchip v2.0
Manufactured by Illumina
The Illumina Human MicroRNA expression beadchip (v2.0) is a microarray platform designed for the detection and quantification of human microRNA expression. It provides a comprehensive coverage of human microRNAs, allowing for the simultaneous measurement of thousands of microRNA transcripts.
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Lab products found in correlation
2 protocols using human microrna expression beadchip v2.0
1
Comprehensive miRNA Expression Profiling
2
Profiling Tumor Biopsy miRNA Expression
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RNA was isolated from pretreatment tumor biopsy specimens as described previously.15 Briefly, miRNA was extracted from pretreatment biopsy specimens using an mirVana miRNA Extraction Kit (Ambion). A NanoDrop Spectrophotometer (Thermal Scientific) was used to quantify the specimens as well as assess the purity of the RNA. In addition, the spectrum of each specimen was visually analyzed to ensure that all profiled samples had a normal spectral profile. These samples were analyzed for miRNA expression using 3 separate platforms: TaqMan Human MicroRNA Card Set v3.0 (Applied Biosystems), Fluidigm 48.48 Dynamic Array (Fluidigm), and Illumina Human MicroRNA expression beadchip v2.0 (Illumina) per the manufacturers' instructions. Our discovery cohort was assayed using a TaqMan array, the model cohort was assayed using a Fluidigm array, and our validation cohort was examined using an Illumina array. This was done to ensure validity across multiple assay platforms. Each miRNA assay was tested in duplicate, and the mean Ct value was normalized to the averaged expression of spike-in miRNAs cel-39 and cel-54 and then subjected to analysis using the 2−ΔΔCt method.16 (link) For the Taqman array, miRNAs detected in less than 20% of samples were excluded from analysis.
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