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7 protocols using cfx opus

1

SARS-CoV-2 RT-PCR Detection Protocols

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As described in our previous study [11 ], RT-PCR was performed based on diagnostic kits with CE IVD certification – Viasure SARS-CoV-2 Real-Time PCR Detection Kit (Certest Biotec S.L., San Mateo de Gallego, Spain), MediPan 2G + Fast COVID Kit (Medicofarma, Radom, Poland), 2019 Novel-Coronavirus [2019-nCOV] Triplex RT-qPCR Detection Kit (Vazyme, Nanjing, China), MutaPlex Coronavirus Real-Time-RT-PCR Kit (Immunodiagnostic, The Boldons, Great Britain), XpertXpress SARS-CoV-2 and Xppert Xpress SARS-CoV-2/Flu/RSV (Gene Xpert, Sunnyvale, California, USA) – in suitably thermal conditions, as recommended by the manufacturers, on BioradCFX 96 and BioradCFX Opus thermal cyclers (BioRad, California, USA) and Aria MX and Aria DX (Agilent Technologies, California, USA). The test was interpreted according to the manufacturers’ recommendations.
The RT-PCR tests had the necessary certification (CE IVD) for use for routine diagnostics. Several diagnostic tests were used due to (1) the lack of availability of one type of diagnostic test on the market that would have been able to satisfy the need for mass testing, and (2) the need to confirm the result (in the case of a diagnostically questionable result) with a test from another manufacturer.
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2

Quantitative Gene Expression Analysis in Honey Bees

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RNA was prepared from the midgut tissue of the bees, as previously described [25 (link)]. Midgut tissue was manually crushed with a disposable pestle in Trizol Reagent (Invitrogen, San Diego, CA, USA) and RNA was then extracted as per the manufacturer’s instructions. RNA was then DNaseI-treated by RQ1 RNase-Free DNase (Promega, Madison, WI, Canada) and cDNA was synthesized using approximately 1 μg of RNA and the High-Capacity cDNA Reverse Transcription Kit with RNase Inhibitor (Applied Biosystems, Foster City, CA, USA). For the quantitative PCR (qPCR) reactions to determine the expression levels of the gene of interest, 1 μL of cDNA was used as a template, in conjunction with PowerUp SYBR Green Master Mix (Applied Biosystems, Foster City, CA, USA) and appropriate primers. Reactions were run in a LightCycler 480 thermal cycler (Basel, Switzerland) or Bio-Rad CFX Opus (Bio-Rad, Hercules, CA, USA) using the PCR conditions stated above. The primer sequences targeting the transcripts of the gene of interest were from [25 (link)]. The difference between the threshold cycle number for β-actin and that of the gene of interest was used to calculate the level of that gene relative to β-actin using the typical 2(−ΔCT) method [23 (link)]. All qPCR data represent the expression values from individual bees (sample sizes found in figure legends) and is displayed as the mean ± SEM.
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3

Quantitative PCR Analysis of Bee Midgut Genes

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RNA was prepared from bees’ midgut tissue as previously described (21 (link)). Midgut tissue was manually crushed with a disposable pestle in Trizol Reagent (Invitrogen, San Diego, CA, USA), and RNA was then extracted as per the manufacturer’s instructions. RNA was then DNase treated using RQ1 RNase-Free DNase I (Promega, Madison, WI, USA) and cDNA was synthesized using approximately 1 µg of RNA with the High-Capacity cDNA Reverse Transcription Kit with RNase Inhibitor (Applied Biosystems, Foster City, CA, USA). For qPCR reactions to determine the expression levels of genes of interest, 1 µL of cDNA was used as a template in conjunction with PowerUP SYBR Green Master Mix (Applied Biosystems, Foster City, CA, USA) and appropriate primers in a 20 µL reaction. Reactions were run in a LightCycler 480 thermal cycler (Basel, Switzerland) or Bio-Rad CFX Opus (Bio-Rad, Hercules, CA, USA). Primer sequences targeting transcripts of genes of interest are from references (21 (link), 22 (link)). The difference between the threshold cycle number for β-actin and that of the gene of interest was used to calculate the level of that gene relative to β-actin using the typical 2(-ΔCT) method (17 (link)). All qPCR data represent expression values from individual bees (sample sizes found in figure legends) and is displayed as mean ± SEM.
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4

Transcriptional Profiling of SAH Rat Brain

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TRIzol reagent (ThermoFisher Scientific Corporation, Shanghai, China) was used to extract total RNA from the right temporal lobe brain tissue of rats 24 h after SAH, and the extracted RNA (1 μg) was reversely transcribed into cDNA using PrimeScript™ RT reagent Kit (Takara Biomedical Technology Corporation, Beijing, China). RT‐qPCR was performed on CFX Opus (Bio‐Rad Laboratories Corporation, Shanghai, China) using Talent qPCR PreMix (SYBR Green) (Tiangen Biochemical Technology Corporation, Beijing, China). The complete reactions were subjected to the following program of thermal cycling: 40 cycles of 5 s at 95°C and 15 s at 60°C. Housekeeping gene Gapdh was used for the normalisation of data before the calculation was performed with the 2−ΔΔCt method. Primer sequences (forward and reverse, respectively) were exhibited as follows: CD14(GCGTCGACGCCACCATGAGCCGGCAGGTGGT; GCGGATCCCTACTTGGCCTGAACAGTCTCCT), SPP1(ATCTCACCATTCGGATGAGTCT; ATCTCACCATTCGGATGAGTCT), PRDX5(CCAATCAAGACACACCTGCC; TCTTGAGACGTCGATTCCCA) and GPNMB(GAAATTCATCCGACGAAAC; ATTGGTGGAAACAAACAGG).
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5

EHDV Serotyping by One-Step qRT-PCR

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The samples that were positive during the initial EHDV detection were then tested for serotypes 1, 2, and 6. The reactions were performed in technical triplicates using the Superscript III/ Platinum Taq One-Step qRT-PCR Kit (Invitrogen, Waltham, MA, USA). The primers and probes (LGC Biosearch Technologies, Petaluma, CA, USA) were specific to the VP2, seg-2 region of each virus serotype [24 (link)] (Supplementary Table S1). The samples were amplified on a Bio-Rad CFX OPUS real-time PCR machine under the following conditions: 55 °C for 30 min, 95 °C for 10 min, and 50 cycles at 95 °C for 30 s and 60 °C for 1 min. The data were analyzed using Bio-Rad CFX Maestro qPCR software.
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6

Detailed qPCR and ddPCR protocols

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The details of all commercial reagents, plasticware and instruments are listed in Table 1.
The recipes for buffers 19 (B19), 25 (B25), 27 (B27), 47 (B47) and 50 (B50) are shown in Table 2. qPCR reactions were carried out using four different qPCR instruments: 96-well cyclers CFX Connect and a CFX Opus (BioRad, Watford, UK), a 48-sample Mic magnetic induction instrument (Bio Molecular Systems, London, UK) or a 48-well Techne PrimePro 48 cycler (Cole Palmer, St. Neots, UK). The ddPCR runs were carried out on a BioRad QX200 instrument.
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7

Angiotensin II Regulation of RNA Expression

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HUVECs were cultured and treated with either vehicle or Ang II for 24 h and then total RNA was extracted using TRIzol. Complementary DNA was synthesized using Quantitect reverse transcription kit (Qiagen, Germantown, Maryland, USA) and qPCR was performed using forward and reverse primers (Supp. Table 1, https://links.lww.com/HJH/B983) and CFX Opus (Biorad, Hercules, California, USA) qPCR machine. Data was analysed using 2 -ΔΔCt method and Student's t-test. A value of P less than 0.05 was considered statistically significant.
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