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7 protocols using sensimix sybr no rox one step kit

1

Quantitative Real-Time PCR Profiling

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RNA was isolated and purified using a microRNA NucleoSpin® Kit (Macherey & Nagel, Düren, Germany). The concentration and purity of the isolated RNA was measured and controlled using a NanoDrop spectrophotometer (Thermo Scientific, Peqlab Biotechnologie GmbH). The primers for qRT-PCR were designed using Primer3 Input software (v. 0.4.0, Whitehead Institute for Biomedical Research, Cambridge, MA, USA, Table S2) and purchased from Eurofins MWG (Ebersberg, Germany). One-step qRT-PCR was performed using a SensiMix™ SYBR No-ROX One-Step Kit (Bioline, Luckenwalde, Germany), including SYBR Green detection on a RotorGene 6000 cycler (Corbett Life Science, Sydney, Australia). The relative mRNA levels were calculated with an external standard curve using the average expression levels of housekeeping genes (Rn18S or β-actin).
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2

Extraction and Analysis of RNA from Liver and Adipose Tissue

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Total RNA from the liver was isolated using the miRNA NucleoSpin® Kit (Macherey & Nagel, Düren, Germany) and quantified as described previously [32 (link), 55 (link)]. Total RNA from epididymal white adipose tissue (VAT) was isolated by optimized guanidine isothiocyanate/phenol-chloroform extraction using peqGOLD TriFastTM (VWR International, Leuven, Belgium). The primers for the qRT-PCR were designed using Primer3 Input software version 4.1.0 (https://primer3.ut.ee/) and purchased from Eurofins MWG (Ebersberg, Gemany) (Table 1). The qRT-PCR was performed using the SensiMix™ SYBR No-ROX one step kit (Bioline, Luckenwalde, Germany) on a Rotorgene 6000 cycler (Corbett Life Science, Sydney, Australia). Target gene mRNA expression was calculated using an external standard curve and related to the housekeeper Rn18S (for liver) or the mean of Rn18S and Gt2b (for VAT).
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3

Quantification of Glucose Metabolism Genes

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Total RNA was isolated and purified from the treated cells using QIAzol lysis reagent (QIAGEN Sciences, USA) and RNA clean and Concentrator-25 (Inqaba Biotech, SA). Double stranded cDNA was synthesized from 3 μg of the total RNA using Superscript Reverse Transcriptase III (Invitrogen, USA). Real time quantitative PCR was done in triplicate using Rotor gene-3000 quantitative real-time PCR machine using Sensi Mix SYBR No-ROX One-Step Kit (Bioline, UK). The primers used were mouse Glut4 gene (Forward primer- 5’ GCA GCG AGT GAC TGG AAC A 3′; Reverse primer- 5’CCA GCC ACG TTG CAT TGT AG 3′), Nrf-1 gene (Forward primer- 5′ AAA CAC AAA CTC AGG CCA CC 3′; Reverse primer-5’ CCA TCA GCC ACA GCA GAG CA 3′) and Mef2a gene (Forward primer-5′ GTG TAC TCA GCA ATG CCG AC 3′; and Reverse primer-5’ AAC CCT GAG ATA ACT GCC CTC 3′). The amplification occurred in a 3-step cycle: denaturation at 95 °C for 5 s, annealing at 60 °C for 10 s, and extension at 72 °C for 15 s. Relative mRNA expression was normalised to mouse Actin reference gene (Forward primer- 5′ GAG ACC TTC AAC ACC CCA GCC 3′; Reverse primer- 5′ GGA GAG CAT AGC CCT CGT AG 3′) and calculated according to relative standard method.
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4

Quantitative RT-qPCR detection of FIPV and H1N1

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The viral RNA was extracted from 100 μL of the harvested cell culture using a QIAamp viral RNA extraction kit (Qiagen, Germany), as per the manufacturer's protocol. Virus-infected and uninfected cells were maintained as positive and negative controls, respectively. The primers for amplification of FIPV and H1N1 (Table 2) were based on the established primers previously designed [20 (link), 21 ], respectively. The reverse transcriptase quantitative real-time PCR (RT-qPCR) was performed using a Bio-Rad CFX96 real-time system (BioRad, USA). The reaction was amplified in a final volume of 25 μL using a SensiMix SYBR No-ROX One-Step Kit (Bioline, UK), which consisted of 12.5 μL 2X SensiMix SYBR No-Rox One-Step reaction buffer, 10 μM forward and reverse primers, 10 units RiboSafe RNase inhibitor, and 5 μL template RNA. Absolute quantification approach was used to quantify qPCR results where a standard curve of a serial dilution of virus was plotted before the quantification. Amount of the virus in the samples was quantified based on this standard curve.
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5

qPCR Quantification of RIOK3 Expression

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RNA was extracted using TRI® reagent (Sigma-Aldrich) and converted to cDNA using a High Capacity cDNA Reverse Transcription Kit (Life Technologies). qPCR was carried out using SensiMix SYBR No-ROX One-Step Kit (BioLine, London, UK) using the following primers RIOK3 F AAGGAGTCTGTTGTCTTTCATGC, RIOK3 R CTTGATGGCACATTCTGTAGGT, HPRT1 F CCAGTCAACAGGGGACATAAA, HPRT1 R CACAATCAAGACATTCTTTCCAGT.
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6

Quantitative RT-PCR Analysis of Liver Gene Expression

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Liver total RNA was isolated using peqGold Trifast®(Peqlab, Erlangen, Germany). RNA concentration and purity were determined by measuring the absorbance at 230, 260 and 280 nm with a NanoDrop 2000TM (Thermo Fisher, Waltham, USA). RNA aliquots were stored at −80 °C until PCR analysis. One-step quantitative reverse transcriptase PCR was carried out with the SensiMix™ SYBR No-ROX one step kit (Bioline, Luckenwalde, Germany) and with SybrGreen detection using the Rotorgene 6000 cycler (Corbett Life Science, Sydney, Australia). Relative mRNA levels of target genes were normalised to Gapdh and Actb gene expression and related to the AL-control. Mean value of expression in the AL-control group was set to an arbitrary unit of 1. All data are represented as means +/− SEM (n ≥ 8). See primers in Table 1.

Primers used for quantitative reverse transcriptase PCR.

PrimerForward (5′-…-3′)Reverse (5′-…-3′)
ActbGACAGGATGCAGAAGGAGATTACTTGATCCACATCTGCTGGAAGGT
Foxo3TTGTCCCAGATCTACGAGTGGCCGTGCCTTCATTCTGAAC
GapdhCCGCATCTTCTTGTGCAGTGGCAACAATCTCCACTTTGC
Hmox1GAGCCTGAATCGAGCAGAACAGCCTTCTCTGGACACCTGA
Pck1AGCCTTTGGTCAACAACTGGTGCCTTCGGGGTTAGTTATG
Pgc-1αTGCCCAGATCTTCCTGAACTTCTGTGAGAACCGCTAGCAA
Sirt1GTCTCCTGTGGGATTCCTGAACACAGAGACGGCTGGAACT
TnfαTCGTAGCAAACCACCAAGTGAGATAGCAAATCGGCTGACG
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7

qPCR Quantification of RIOK3 Expression

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RNA was extracted using TRI® reagent (Sigma-Aldrich) and converted to cDNA using a High Capacity cDNA Reverse Transcription Kit (Life Technologies). qPCR was carried out using SensiMix SYBR No-ROX One-Step Kit (BioLine, London, UK) using the following primers RIOK3 F AAGGAGTCTGTTGTCTTTCATGC, RIOK3 R CTTGATGGCACATTCTGTAGGT, HPRT1 F CCAGTCAACAGGGGACATAAA, HPRT1 R CACAATCAAGACATTCTTTCCAGT.
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