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2 protocols using mirneasy mini kit for mirna

1

Quantification of mRNA and miRNA Expression

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Total RNA was extracted using RNeasy mini kit for mRNA and miRNeasy mini kit for miRNA (QIAGEN). 500ng (mRNA) or 50ng (miRNA) was reverse transcribed into cDNA using iScript cDNA Synthesis Kit (Bio-Rad) for mRNA or the TaqMan microRNA Reverse Transcription Kit (Applied Biosystems) for miRNA. For mRNA, cDNA PCR was performed using SYBR Green master mix (Applied Biosystems). For miRNA, cDNA PCR was done using TaqMan Universal Master Mix, no AmpErase UNG (Applied Biosystems) and primers (20X) from the TaqMan MicroRNA Assay. Reactions were run in quadruplicates. Data were normalized to housekeeping genes GAPDH or GUSB for mRNA and RNU48 for miRNA and represented as mean ± SD. For mir-34A methylation analysis, genomic DNA was extracted using DNeasy Blood & Tissue kit (QIAGEN). Bisulfite conversion was performed with EpiTect kit (QIAGEN) and CpG island 157 was amplified by PCR. The PCR products were gel-purified and subcloned into pGEM-T Easy vector (Promega) followed by transformation into competent cells for blue-white screening. 8–10 positive colonies were sequenced with T7 primers. All relevant primer sequences are listed in Supplementary Methods.
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2

RNA Isolation and Microarray Analysis

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RNA isolation was performed according to the manufacturer's instructions using the RNeasy Mini-Kit (Qiagen, Hilden, Germany) for mRNA and miRNeasy Mini-Kit for miRNA (Qiagen). The prepared RNA was preserved at −80 °C. Only samples with RNA integrity number >8.8 for miRNA and >8.7 for mRNA were accepted for further processing.
Array analyses were performed using RNA 6000 Nano LabChipVR reagent set (Agilent Technologies, Boeblingen, Germany), Low RNA Input Linear Amplification Kit PLUS, One-Color (Agilent Technologies), Gene Expression Hybridisation Kit (Agilent) and miRNA Labelling Reagent and Hybridisation Kit (Agilent Technologies).
The Microarray Scanner G2505B (Agilent Technologies) was used for washing and scanning of miRNA and mRNA arrays.
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