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Quantstudio 3 real time pcr system

Manufactured by Bio-Rad
Sourced in United States

The QuantStudio 3 Real-Time PCR System is a laboratory instrument designed for quantitative real-time polymerase chain reaction (qRT-PCR) analysis. It is capable of performing thermal cycling and data collection for nucleic acid amplification experiments.

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8 protocols using quantstudio 3 real time pcr system

1

Quantifying mRNA Expression by qPCR

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Messenger Ribose Nucleic Acid (mRNA) levels were examined by routine real‐time qPCR assay. Total Ribose Nucleic Acid (RNA) from cells and tissues were extracted, respectively, using TRIzol kit (Thermo Fisher). One‐microgram RNA was used for reverse transcription using the PrimeScript RT reagent with gDNA Eraser (Takara; cat# RR047A). qPCR was performed with iQ SYBR Green Supermix (Bio‐Rad; cat# 1708882) and QuantStudio 3 Real‐Time PCR System (Bio‐Rad). Relative mRNA expression was normalized with Actb. Primer sequences are shown in Table S2.
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2

Quantitative Real-Time PCR Protocol

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Total RNA was reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. After cDNA quantification by NanoDrop One (Thermo Fisher Scientific, Waltham, MA, USA), qRT-PCR was performed using Universal iTaq SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA, USA) following the manufacturer’s instructions and using a QuantStudio™ 3 Real-Time PCR System. We used 5 µL SYBR Green Mix (2×), 3 µL of 600 nM forward and reverse primers mix (Thermo Fisher Scientific, Waltham, MA, USA) and 2 µL of 90–100 ng/mL cDNA sample per reaction. Cycles consisted of polymerase activation and DNA denaturation at 95 °C for 3 min, 40 cycles of amplification and annealing–extension at 95 °C for 15 s followed by 60 °C for 1 min, respectively. All primers used for gene expression analysis are described in Table 1. GAPDH was used as a housekeeping gene to calculate the relative quantification by the ∆∆CT method.
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3

Quantitative RT-PCR Analysis of BAT mRNA

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BAT mRNA was prepared from whole BAT tissue using Trizol (Invitrogen, 15596018). 1μg of RNA was used to synthesize cDNA using the Maxima H Minus cDNA Synthesis Master Mix (Thermo Scientific, M1662) and with an extension time of 60 min. at 50°C. qPCR was performed using SsoAdvanced Universal SYBR Green Supermix (Bio-Rad, 1725270) using the following parameters:

95°C- 10 min.

95°C- 30 sec.

60°C- 1 min.

40 cycles of steps 2 and 3

95°C- 15 sec.

Amplification was performed using a QuantStudio 3 Real-Time PCR System. Analysis was performed using the 2ΔΔCT method and data were normalized relative to 18SrRNA expression. Primer sequences can be found in Table S6.
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4

Quantifying Mitochondrial Dynamics Genes

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mRNA levels of genes in tibialis anterior from WT and SKMiPLA2γKO mice were determined by quantitative real-time PCR, which was performed by the Genome Engineering and Stem Cell Center (GESC) at Washington University. Briefly, total RNA was extracted from TA tissues using TRIzol™ Reagent (Thermo Fisher Scientific). Quantitative RT-PCR was performed as one-step using Reliance One-Step Multiplex RT-qPCR Supermix (Bio-Rad) on QuantStudio™ 3 Real-Time PCR System according to manufacturer’s instructions. The commercially available primers for the following mouse genes were purchased from Thermo Fisher Scientific: Drp1 (aka Dnm1l), Mm01342903_m1; Mfn1, Mm00612599_m1; and Opa1, Mm00453879_m1. Tissue mRNA levels were normalized to the level of an internal reference gene (mouse Ppia) in the same tissue sample. Relative gene expression levels were calculated using the 2-ΔΔCt method.
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5

Inflammatory Cytokine Profiling in THP-1 Cells

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THP‐1 cells (1 × 106 cells per well) were cultured in 6‐well plates overnight. DAMP media (1 mL) was mixed with culture media (1 mL) and added to each well. After incubation for 24, 48, and 72 h, the medium was collected for ELISA, and the cells were washed three times with PBS. Total RNA was isolated with a Direct‐zol RNA Miniprep kit (Zymo Research, USA), and the concentration of the isolated RNA was measured with a Denovix DS‐11+ spectrophotometer. Equal amounts of RNA in different samples were reverse transcribed into cDNA with an iScript cDNA Synthesis Kit (Bio‐Rad, USA). cDNA was amplified with SsoAdvanced Universal SYBR Green Supermix (Bio‐Rad, USA) using a QuantStudio 3 Real‐Time PCR System. The primer sequences are shown in Table S3, Supporting Information. Media collected from THP‐1 or RAW 264.7 cells was centrifuged to remove cells and debris. The levels of TNF‐α, IL‐1β, and IL‐6 were measured using ELISA kits (Invitrogen, USA).
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6

Quantitative PCR Analysis of Muscle Atrophy

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One microgram of RNA was reverse transcribed using iScript reaction mix (#170-8890, BioRad) and a MasterCycler Gradient thermocycler (EP-MC, Marshall Scientific). cDNA was then diluted 1:7 in nuclease free water and pipetted into a 96 well plate with mouse glyceraldehyde-3-phosphate dehydrogenase (GAPDH), MuRF-1, and Atrogin-1 primer probes (GAPDH: 4352339E, MuRF-1: 4331182, Atrogin-1: 4331182), and TaqMan fast advanced master mix (#4444556, ThermoFisher). The qPCR reaction was performed on the QuantStudio3 Real Time PCR system (Bio-rad) and data were analyzed using the 2− ΔΔCT method with GAPDH as a reference gene 42 (link) following verification that GAPDH was stable across time points and between limbs in mouse quadriceps.
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7

Quantifying Messenger RNA Levels by RT-qPCR

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Messenger ribonucleic acid (mRNA) levels were examined by RT-qPCR assay. Total ribonucleic acid (RNA) from cells or tissues was extracted using TRIzol kit (TAKARA, Beijing), respectively. 1 mg of RNA was reverse transcribed using HiScript® III All-in-one RT SuperMix (Vazyme, R333-01) reagent. RT-qPCR was performed using ChamQ Universal SYBR qPCR Master Mix (Vazyme, Q711-02) and QuantStudio 3 Real-Time PCR System (Bio-Rad). The relative amount of each gene was normalized to the amount of β-actin.
The ΔΔ -Ct algorithm was used for RT-qPCR analysis. Primer sequences are shown in Table S1.
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8

RNA Extraction and qRT-PCR Analysis

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Total RNA was extracted using the RNeasy Kit (Qiagen) according to the manufacturer’s instructions. Purified RNA was used for RT-PCR with the High-Capacity cDNA Reverse Transcription Kit (Thermo fisher). qPCR was performed using iTaq Universal SYBR Green Supermix (Bio-Rad) and run on QuantStudio 3 Real-Time PCR System. The primers sequences used for qRT-PCR are listed in Supplementary Table 1.
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