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Cfx96 touch real time pcr detection system machine

Manufactured by Bio-Rad

The CFX96 Touch™ Real-Time PCR Detection System is a laboratory instrument designed for performing real-time polymerase chain reaction (PCR) analysis. The system is capable of detecting and quantifying specific nucleic acid sequences in samples during the amplification process.

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3 protocols using cfx96 touch real time pcr detection system machine

1

Validating Patient-Specific Structural Variants

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In order to validate selected patient-specific structural variants, qRT-PCR was performed using SsoFast™ Evagreen® Supermix (Bio-Rad Laboratories Inc., Hercules, CA, USA) and Primer3-designed PCR primer pairs (0.5μM) (Metabion) spanning the SVs (qRT-PCR primer sequences are available in S5 Table). An internal control primer-pair at 18q12.2 was selected to confirm the efficiency of the reaction and normalize the results. All reactions for each primer pair were run in triplicates on a CFX96 Touch™ Real-Time PCR Detection System machine (Bio-Rad Laboratories, Inc.), and results were analyzed using the Bio-Rad CFX Manager analysis software (comparative Ct method).
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2

Quantitative Analysis of Gene Expression

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Prior to total RNA-extraction cells were washed once in PBS (Sigma). Total RNA was extracted using the Omega BIO-TEK E.Z.N.A.® Total RNA Kit I (Omega BIO-TEK; Cat.# R6834-02) according to the manufacturer’s instructions. DNA digestion was performed on-column using the Qiagen RNase-Free DNase Set (Qiagen; Cat.# 79256). cDNA was generated from 1 µg RNA (assessed by Nanodrop2000 (Thermo Fisher Scientific) measurement) using the Applied Biosystems High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems; Cat.#4368814). Real-time qPCRs were performed in 96-well plates using the PrecisionPLUS qPCR Mater Mix (Primer Design; Cat.#4368814) and the CFX96 Touch Real-Time PCR Detection System machine (BIO-RAD) and BIO-RAD FX96 Touch Real-Time PCR Detection System - CFX Maestro Software. The expression of transcripts was normalized to expression of Large Ribosomal Protein (RPLPO). Data analysis was performed using the Cycles threshold (ddCt) method and expressed as mRNA relative expression ddCt. The following TaqMan probes (Applied Biosystems) were used for qPCR analysis: RPLPO (Hs99999902_m1), SBNO2 (ISO1/ISO2) (Hs00922127_m1), SBNO2 (ISO1) (Hs00209130_m1), IL20 (Hs00218888_m1), IL23A (Hs00900828_g1), IL24 (Hs01114274_m1), CXCR2 (Hs00174304_m1), CXCR4 (Hs00976734_m1), KREMEN1 (Hs00230750_m1)
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3

Klk6 Knockout Mouse Generation

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Mice genetically deficient in Klk6, or wild type litter mates, were used in all in vivo experiments. Both male and female mice were used and ranged in age from postnatal day (P) 0 to 90 days. Coding exons 3 and 4 of the Klk6 gene were deleted in knockouts by inserting a “universal docking site” cassette (Samantha Sykioti et al. 2020 ) (Dr. A. Nagy, Mount Sinai, Toronto, Canada) and were a generous gift from Dr. G. Sotiropoulou, University of Patras, Greece. A schematic diagram of the transgenic cassette and the PCR genotyping strategy were recently published (Pampalakis et al. 2017 (link)). Mice with Klk6 knockout are viable, fertile and have no prominent phenotypic abnormalities. Wild-type (Klk6+/+) littermates were used as controls for all experiments. Mice were genotyped using probes and primers as listed in Table 1, using iTaq™ Universal Probes One-Step Kit or the iTaq™ Universal SYBR Green One-Step Kit (1725141 or 1725151, respectively, Bio-Rad) on a CFX96 Touch Real-Time PCR Detection system machine (Bio-Rad). Klk6 knockout, Klk6 wild type and C57BL/6J mice (#000664, Jackson Laboratory Bar Harbor, ME) were used for the study of Klk6 in primary oligodendrocyte progenitor cell cultures. All animal experiments were carried out with adherence to NIH Guidelines for animal care and safety and were approved by the Mayo Clinic Institutional Animal Care and Use Committee.
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