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10 protocols using topscript one step rt pcr drymix

1

Quantitative RT-PCR for ESM-1 Expression

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Extracted total RNA was applied to RT-PCR using TOPscript One-step RT-PCR Drymix (Enzynomics, Daejeon, Korea) according to the manufacturer’s instructions. The sequences of the primers used were as follows: hESM-1 forward: 5′-GC CCT TCC TTG GTA GGT AGC-3′ and reverse: 5′-TG TTT CCT ATG CCC CAG AAC-3′; mESM-1 forward: 5′-ACT CCT GGT ACC TCT GCA CC-3′ and reverse: 5′- CAT TCC ATC CCG AAG GTG CC-3′; hGAPDH forward: 5′- TCA ACA GCG ACA CCC ACT CC-3′ and reverse: 5′-TGA GGT CCA CCC TGT TG-3′; and mGAPDH forward: 5′-GCT GAG TAC GTG GAG-3′ and reverse: 5′-CAT ACT TGG CAG GTT TCT-3′. Thirty cycles of amplification were performed under the following conditions: melting at 95 °C for 30 s, annealing at 57.5 °C or 60 °C for hESM-1 or mESM-1, respectively, for 30 s, and extension at 72 °C for 30 s.
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2

SFTS Virus Detection in Patient Sera

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Sera were isolated from eleven SFTS patients admitted to Jeonbuk National University Hospital. Serum samples were obtained from blood within six hours following confirmation of infectious with the SFTS virus. Laboratory-confirmed SFTS virus infection was defined according to the following criteria: (1) clinical symptoms (e.g., fever), (2) epidemiological evidence supporting the possibility of a tick bite, and (3) identification of viral RNA through reverse transcription polymerase chain reaction (RT–PCR). To detect SFTSV RNA, RNA was extracted from the serum using a QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany) according to manufacturer instructions. One-step RT–PCR was performed using a ToPscript™ One-step RT PCR DryMix (Enzynomics, Daejeon, Korea) with the primers MF3 (5′- GATGAGATGGTCCATGCTGATTCT-3′) and MR2 (5′- TCATGGGGTGGAATGTCCT CAC-3′).
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3

Total RNA Extraction and RT-PCR Analysis

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Total RNA from cells was then extracted using TRIzol reagent (#15596018, Thermo Fisher Scientific) as described in the manufacturer’s protocol. All primers were obtained from Bioneer (Deajeon, Korea), and RT-PCR was performed using TOPscript One-step RT-PCR Drymix (#RT421, Enzynomics, Deajeon, Korea) according to the manufacturer’s instructions. The primer sets are listed in Table 1. Amplification was performed under the following conditions: 30 cycles of denaturation at 95 °C for 30 s, annealing at 58 °C for 30 s, and extension at 72 °C for 1 min.
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4

SFTSV Detection via Nested PCR

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To detect SFTSV, nested PCR was performed using MF3 and MR2 primers to target the M fragment (Table 2). Reactions were performed in a total volume of 20 μL, containing TOPscript One-step RT PCR DryMix (Enzynomics, Republic of Korea), 1 μL of each primer (10 pmol/μL), 5 μL of template RNA, and 13 μL of distilled water (DW). The reaction conditions comprised cDNA synthesis steps at 50 °C for 30 min and at 95 °C for 10 min. Following this, 35 cycles of 95 °C for 20 s, 58 °C for 40 s, and 72 °C for 30 s were performed, followed by a final extension at 72 °C for 5 min. For the second amplification, reactions were performed in a total volume of 20 μL, containing 10 μL of 2× TOPsimple DyeMix (aliquot)-HOT (Enzynomics, Republic of Korea), 1 μL of each primer (10 pmol/μL), 1 μL of 1stPCR product, and 7 μL of DW, using MMF3 and MMF2 primers. Reaction conditions comprised a denaturation step at 94 °C for 5 min, followed by 35 cycles of 94 °C for 20 s, 59 °C for 20 s, and 72 °C for 20 s. After this, a final extension was performed at 72 °C for 5 min.
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5

RT-PCR Quantification of hP2Y2R Expression

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RT-PCR was performed using TOPscript One-step RT PCR Drymix (Enzynomics, Daejeon, Korea), according to the manufacturer’s instructions. The primer sets used were as follows: hP2Y2R, 5′-GTG CTC TAC TTC CTG GCT-3′ and 5′-CTG AAG TGT TCT GCT CCT AC-3′ and hGAPDH, 5′- TCA ACA GCG ACA CCC ACT CC-3′ and 5′- TGA GGT CCA CCA CCC TGT TG-3′.
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6

Quantifying Inflammatory Mediators in Cells

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Recombinant human TNF-α protein and human IL-1β/IL-1F2 Quantikine ELISA kits were purchased from R&D Systems (Minneapolis, MN, USA). ATP, apyrase, anti-β-actin (#A2066) antibody, and 4′,6-diamidine-2′-phenylindole dihydrochloride (DAPI) were obtained from Sigma-Aldrich (St. Louis, MO, USA). Anti-NLRP3 (#ab214185), anti-NLRC4 (#ab99860), and anti-cleaved caspase-1 (#ab179515) antibodies and human VEGF-A ELISA kits were purchased from Abcam (Cambridge, United Kingdom), and anti-ASC (#13833) antibody was obtained from Cell Signaling Technology (Beverly, MA, USA). TOPscript One-step RT PCR Drymix was purchased from Enzynomics (Daejeon, Korea). Negative control siRNA (control siRNA) and NLRP3, NLRC4, ASC, caspase-1, and P2Y2R siRNA were obtained from Bioneer (Daejeon, Korea), and Lipofectamine 3000 reagent, TRIzol reagent, and anti-P2Y2R (#PA1-46150) antibody were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Hybond-P+ polyvinylidene difluoride membrane was obtained from GE Healthcare (Chicago, IL, USA), and Clarity Western enhanced chemiluminescence (ECL) substrate was purchased from Bio-Rad (Hercules, CA, USA). BD Matrigel basement membrane matrix (Matrigel) was obtained from BD Bioscience (Franklin Lakes, NJ, USA), and cell culture inserts for 24-well plates (8.0 µm, Translucent PET membrane) were purchased from Corning (Corning, NY, USA).
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7

Quantification of P2Y2 Receptor mRNA

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Total RNA was extracted from the cells using TRIzol reagent (Thermo Fisher Scientific), and RT-PCR was performed using TOPscript One-step RT PCR Drymix (Enzynomics, Daejeon, Korea), according to the manufacturer’s instructions. The primer sets used were as follows: hP2Y2R forward, 5′-GTG CTC TAC TTC CTG GCT-3′ and reverse, 5′-CTG AAG TGT TCT GCT CCT AC-3; ′ and hGAPDH forward, 5′- TCA ACA GCG ACA CCC ACT CC-3′ and reverse, 5′-TGA GGT CCA CCA CCC TGT TG-3′. Thirty cycles of amplification were performed under the following conditions: Melting at 95°C for 30 sec, annealing at 56°C for 30 sec and extension at 72°C for 30 sec.
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8

Gene Expression Analysis of P2Y2 Receptor

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Total RNA was extracted using TRIzol Reagent (Invitrogen), and RT-PCR was performed using the TOPscript One-step RT PCR DryMIX (Enzynomics, Daejeon, Korea) according to the manufacturer's instructions. The primer sets used were as follows: hP2Y2R, 5′-GTG CTC TAC TTC CTG GCT-3′ and 5′-CTG AAG TGT TCT GCT CCT AC-3′ and hGAPDH, 5′- TCA ACA GCG ACA CCC ACT CC-3′ and 5′- TGA GGT CCA CCA CCC TGT TG-3′. Thirty cycles of amplification were performed under the following conditions: melting at 95°C for 30 sec, annealing at 56°C for 30 sec, and extension at 72°C for 30 sec.
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9

Quantifying Adenosine Receptor Expression

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Total RNA was extracted using TRIzol reagent (15596018, Thermo Fisher Scientific, Rockford, IL, USA). All primers were obtained from Bioneer, and RT-PCR was performed using TOPscript One-step RT-PCR Drymix (RT421, Enzynomics, Daejeon, Korea) according to the manufacturer’s instructions. The primer sets were as follows: hA1R, forward 5′-TCCCTCTCCGGTACAAGATG-3′ and reverse 5′-GCTGCTTGCGGATTAGGTAG-3; hA2AR, forward 5′-AGCTGAAGCAGATGGAGAGC-3′ and reverse 5′-AGGGATTCACAACCGAATTG-3; hA2BR, forward 5′-CAGCGGGAGATCCATGCAG-3′ and reverse 5′-CGGTTCCGGTAAGCATAGACAAT-3; hA3R, forward 5′-TACCCACGCCTCCATCATGT-3′ and reverse 5′-GGGGTCAATCCCACCAGGA-3; hCD39, forward 5′-CTGATTCCTGGGAGCACAT-3′ and reverse 5′-GACATAGGTGGAGTGGGAGAG-3; hCD73, forward 5′-GCCTGGGAGCTTACGATTTTG-3′ and reverse 5′-TAGTGCCCTGGTACTGGTCG-3; hGAPDH, forward 5′-TCAACAGCGACACCCACTCC-3′ and reverse 5′-TGAGGTCCACCACCCTGTTG-3. Thirty cycles of amplification were performed under the following conditions: melting at 95 °C for 30 s, annealing 57.5 or 60 °C for 30 s, and extension at 72 °C for 1 min.
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10

Quantitative RT-PCR of ESM-1 in Breast Cancer

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Total RNA was extracted from breast cancer cells (1 × 106 cells) using TRIzol reagent (15596018, Thermo Fisher Scientific, Waltham. MA, USA) according to the manufacturer’s protocol. RT–PCR was conducted using TOPscript One-step RT–PCR Drymix (RT421, Enzynomics, Daejeon, Korea) by the manufacturer’s instructions. Human ESM-1 and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) primers were purchased from Bioneer (Deajeon, Korea), and the sequences of these primers were as follows: hESM-1 forward, 5′-GC CCT TCC TTG GTA GGT AGC-3′, and reverse, 5′-TG TTT CCT ATG CCC CAG AAC-3′, and hGAPDH forward, 5′- TCA ACA GCG ACA CCC ACT CC-3′, and reverse, 5′-TGA GGT CCA CCC TGT TG-3′. Amplification was conducted under the following conditions: 27 cycles of denaturation at 95 °C for 30 sec, annealing at 57.5 °C for 30 sec, and extension at 72 °C for 1 min.
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