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9 protocols using cyclescript rt premix

1

Gene Expression and Protein Analysis

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Total RNA was isolated and purified using TRIzol reagent (Invitrogen, #15596026) according to the manufacturer's protocol. cDNA was prepared to employ a CycleScript RT premix (Bioneer, #K-2044-CFG). All primer sequences are listed in Table 1. Expression levels were calculated using a SensiFAST SYBR Lo-ROX Kit (Bioline, #BIO-94020) and a commercial detection system (BioRad, #CFX96).
Total proteins were extracted into RIPA buffer (Thermo Fisher Scientific, #89900) containing a phosphatase inhibitor (Sigma-Aldrich, #4906845001) and a protease inhibitor (Roche, #43693159001), subjected to 10–16% (w/v) Tris-glycine SDS-PAGE, transferred to PVDF membranes using Iblot 2 NC ministacks (Invitrogen, #IB23002), and the membranes blocked with 5% (w/v) skim milk. The primary antibodies were anti-pAMPK (Cell Signaling Technology, #2531S), anti-AMPK (Cell Signaling Technology, #5831S), anti-pACC (Cell Signaling Technology, #3661S), anti-ACC (Cell Signaling Technology, #3662S), and anti-GAPDH (Cell Signaling Technology, #2118S) diluted 1:1000 (primary antibodies) or 1:5000 (secondary antibodies) in TBST (Biosesang, #HT2007) containing 5% (w/v) skim milk. The membranes were then incubated with a peroxidase-conjugated anti-rabbit secondary antibody and signals quantitated using the Immobilion Western Chemiluminescent HRP Substrate (Millipore, #WBKLS0500).
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2

Quantification of mRNA Levels in MEFs

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Total RNA was isolated from wild-type and CRBN−/− MEFs by TRIzol reagent (Invitrogen), according to the manufacturer's protocol. Complementary DNA (cDNA) was synthesized using CycleScript RT PreMix (Bioneer). mRNA levels were measured using TB Green™ Premix Ex Taq™ (TaKaRa) and Thermal Cycler Dice Real-Time System. The following primers were used for amplification. p21, forward: 5′ AAT CCT GGT GAT GTC CGA CC -3′, and reverse: 5′-AAA GTT CCA CCG TTC TCG G-3′; 18s rRNA, forward: 5′-GTA ACC CGT TGA ACC CCA TT-3′, and reverse: 5′-CCA TCC AAT CGG TAG TAG CG-3′. Expression was normalized to 18 s rRNA levels.
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3

Isolation and Analysis of Mouse Ovarian RNAs

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Ovaries were punctured with a sterile blade and germinal vesicle (GV) oocytes were collected in M2 medium supplemented with 2.5 μM milrinone (Sigma-Aldrich, Missouri, USA) to maintain them at the germinal vesicle (GV) stage. After PMSG injection, we used a syringe to penetrate the ovary to obtain granulosa cells. Granulosa cells were washed with M2 medium and transferred to PCR tubes. Total RNA from the mouse ovaries were prepared using a miRNeasy Mini Kit (Qiagen, Hilden, Germany). Briefly, ovaries were ground in liquid nitrogen and homogenized in RLT buffer (Qiagen, Hilden, Germany) supplemented with 1% β-mercaptoethanol. The supernatant, mixed with 70% ethanol, was transferred into mini spin columns and total RNA was collected. For the isolation of total RNAs from GV oocytes and cumulus cells, ~100 GV oocytes and cumulus cells from three mice were prepared and the total RNA was isolated using a miRNeasy Micro Kit (Qiagen, Hilden, Germany), in the same manner as the miRNeasy Mini Kit. First-strand cDNA was synthesized with CycleScript RT PreMix (Bioneer, Seoul, Korea). Gapdh was used as an internal standard. The primers for the amplification of CCP1 were described in Kim et al.[8 (link)] and Ccp4 (also known as Agbl1) and CCP6 (also known as Agbl4) were described by Kalinina et al. [10 (link)].PCR products were run on 1.5% agarose gels and visualized using UV illumination.
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4

Transcriptome Analysis Using Total RNA Extraction

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Total RNA was isolated using a Total RNA Extraction Kit (Intron Biotechnology, Korea), according to the manufacturer's protocol. Isolated RNA samples were quantified using a UV–visible spectrophotometer (NanoDrop; Thermo Fisher Scientific, USA). Total RNA (1 μg) was used for first‐strand complementary DNA synthesis using CycleScript RT PreMix (Bioneer, Korea) and Alpha Cycler 1 PCRmax (PCRmax, UK). First‐strand complementary DNA was synthesized by PCR for 1 h at 45°C and 5 min at 95°C. Gene amplification was performed using complementary DNA, primers, and SYBR Blue Master Mix (PCR Biosystems). Gene amplification was performed at 95°C for 2 min and repeated 40 times for 5 s at 95°C and 30 s at 62.5°C. The primers used in this study are listed in Table 1.
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5

Medicinal Herbs for Adipogenesis Study

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Medicinal herbs including Agastache rugosa, Chrysanthemum zawadskii, Mentha arvensis, Perilla frutescens, Leonurus sibiricus, Gardenia jasminoides, and Lycopus coreanus were purchased from Gwangwoo Pharmaceutical (Changwon, Korea). Oil red O (ORO), 3-isobutyl-1-methylxanthine (IBMX), dexamethasone (DEX), insulin, and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and 4-(1,3,3a,4,7,7a-hexahydro-1,3-dioxo-4,7-methano-2H-isoindol-2-yl)-N-8-quinolinyl-benzamide (IWR-1) were purchased from Sigma-Aldrich Co. (St. Louis, MO, USA). Dulbecco’s modified Eagle’s medium (DMEM), penicillin-streptomycin, phosphate-buffered saline (PBS), and bovine calf serum (BCS) were obtained from Welgene Inc. (Daegu, Korea). Fetal bovine serum were purchased from GE Healthcare Bio-Sciences Co. (Piscataway, NJ, USA). TRIzol® was obtained from Life Technologies (Carlsbad, CA, USA), and the Maxime PCR PreMix (i-Taq) was purchased from Intron (Seongnam, Korea). CycleScript RT PreMix was obtained from Bioneer (Daejeon, Korea). All other chemicals were obtained from Sigma-Aldrich Co..
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6

RNA Extraction and RT-qPCR Analysis

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Total RNA was extracted from the cells (1 × 105/48-well plate) using TRIzol™ (15596-026, Thermo Fisher Scientific Inc., Waltham, MA, USA) and acid guanidinium thiocyanate-phenol-chloroform [34 (link)]. The concentration and purity of the RNA defined as the ratio of absorbance at 260 and 280 nm (A260/A280 nm) were measured using an ND-1000 NanoDrop™ spectrophotometer (Qiagen GmbH, Hilden, Germany). Complementary DNA (cDNA) was synthesized from total RNA using Cycle Script RT Premix (dT20, Bioneer, Daejeon, Korea). Sequences of interest were amplified by quantitative real-time PCR (RT-qPCR) using Rotor-Gene SYBR Green PCR Master Mix (204076, Qiagen GmbH) under 30 cycles of 95 °C for 30 s, 55 °C for 30 s, and 72 °C for 30 s [34 (link)]. Relative mRNA expression was calculated using the 2−ΔΔct method [35 (link)] and normalized to that of 18S rRNA. Supplementary Table S1 lists the primer sequences. The experiments were repeated at least three times.
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7

Comprehensive RNA Expression Analysis

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Total cellular RNA was extracted using Trizol reagent (Invitrogen, Grand Island, NY) according to the manufacturer's instructions, and examined for purity and concentration using a photometer (NanoDrop ND). Possible DNA contamination was removed by DNase I (Sigma, St. Louis, MO) incubation for 30 min at 37°C. One µg RNA and primers (Bioneer, CycleScript RT PreMix) were utilized for cDNA synthesis (complementary cDNA synthesis kit, Bioneer, South Korea). Polymerase chain reaction was performed using GeneAmp PCR system 9600 (PerkinElmer Life and Analytical Sciences, Wellesley, MA). Specific primer pairs of Oct-4, Nanog, C-kit, Fragilis, Dazl, Mvh, SCP3, and GDF9 (growth differentiation factor 9) (Table I) were used for PCR reaction. Cycling parameters were as follows: 5 min initial denaturation at 94°C, then 33 cycles at 94°C for 30 s, corresponding to the annealing temperature of primer pairs for 30 s, and 72°C for 1 min.
Ovarian cells from adult ovaries were used as positive controls and liver cells as negative controls. Polymerase chain reaction products were loaded on 2% agarose gel, stained with ethidium bromide, and visualized by UVItec Cambridge-Gel Documentation Systems (CB4 1QB-UK). Expression of β-actin as a housekeeping gene was evaluated as an internal control.
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8

Quantitative PCR for Gene Expression

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Total RNA was extracted from individual TTF-treated samples using the TRIzol extraction method as described by the manufacturer (Invitrogen, Carlsbad, CA, USA). First-strand cDNA was synthesized from 1μg of total RNA using the CycleScript RT PreMix (Bioneer, Daejeon, Korea) according to the manufacturer's protocol. Quantitative PCR was conducted using a standard protocol from the SYBR FAST ROX Low qPCR kit (KAPA, Boston, MA, USA). Primer sequences (human) were as follows: α-SMA, Forward: 5′-GATGGTGGGAATGGGACAAA-3′, Reverse: 5′-GC CATGTTCTATCGGGTACTTC-3′; MMP2, Forward: 5′-TGATGGTGTCTGCTGGAAAG-3′, Reverse: 5′-CTAC AGGACAGAGGGACTAGAG-3′; MMP 9, Forward: 5′-T CACTTTCCTGGGTAAGGAGTA-3′, Reverse: 5′-CTGT CAAAGTTCGAGGTGGTAG-3′; VEGFA, Forward: 5′-C AGGACATTGCTGTGCTTTG-3′, Reverse: 5′-CTCAGA AGCAGGTGAGAGTAAG-3′; HIF1α, Forward: 5′-CCA GTTACGTTCCTTCGATCAG-3′, Reverse: 5′-GTAGTG GTGGCATTAGCAGTAG-3′; GAPDH, Forward:5′-AC CCAGAAGACTGTGGATGG-3′, Reverse: 5′-TCTAGA CGGCAGGTCAGGTC-3′. Signals were normalized to GAPDH.
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9

Quantifying BDNF Expression by qRT-PCR

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RNA was extracted using TRIzol reagent (Invitrogen, #15596026) and reverse transcribed using CycleScript RT premix (Bioneer, #K‐2044‐CFG). The expression of BDNF was measured by real‐time PCR using SYBR Green with low ROX (Enzynomics, #RT500M) and a BioRad #CFX96 cycler. cDNA was amplified using 40 cycles, consisting of denaturation at 95°C for 10 s, annealing at 60°C for 15 s, and elongation at 72°C for 25 s. The primer sequences were: BDNF forward: 5‐TGGCCTAACAGTGTTTGCAG‐3, BDNF reverse 5‐GGATTTGAGTGTGGTTCTCC‐3, 18S forward 5‐GTAACCCGTTGAACCCCATT‐3, and 18S reverse 5‐CCATCCAATCGGTAGTAGCG‐3.
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