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6 protocols using kapa probe fast abi prism qpcr kit

1

Quantitative RT-PCR for Gene Expression

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Immediately after treatment, RNA was isolated with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific). One microgram of total RNA was reverse transcribed with the iScript kit (Bio-Rad). KAPA PROBE FAST ABI Prism qPCR Kit (Kapa Biosystems) and SensiFAST SYBR Hi-ROX (Bioline Reagents) were used for qRT-PCRs that were performed with StepOnePlus or QuantStudio 12K Flex Real-Time PCR System. List of the primers and probes used for qRT-PCR is in Supplementary Table S1. Relative quantities of the target gene messenger RNAs (mRNAs) were normalized against their respective 18S RNA (RNA18S5). All reactions were run in triplicate from samples derived from at least four biological replicates.
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2

Quantifying Gene Expression by qPCR

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The GeneAmp 5700 sequence detection system (ABI, Tokyo) and KAPA PROBE FAST ABI Prism qPCR Kit (Kapa Biosystems, Boston, MA) were used to quantify the levels of HPRT mRNA and CCL5 mRNA. The PCR primer pairs used for real-time PCRs with the KAPA PROBE FAST ABI Prism qPCR Kit were as follows: mouse Hprt primers, 5’-AGCCCCAAAATGGTTAAGGTTG −3’ and 5’-CAAGGGCATATCCAACAACAAAC-3’, probe, 5’-ATCCAACAAAGTCTGGCCTGTATCCAACAC-3’; mouse Ccl5 primers, 5’-CTCCCTGCTGCTTTGCCTAC-3’ and 5’-CGGTTCCTTCGAGTGACAAACA-3’, probe, 5’-TGCCTCGTGCCCACGTCAAGGAGTATT-3’; mouse Ccl20 primers, 5’-ACGAAGAAAAGAAAATCTGTGTGC-3’ and 5’-TCTTCTTGACTCTTAGGCTGAGG-3’, probe, 5’-AGCCCTTTTCACCCAGTTCTGCTTTGGA-3’; mouse cfos primers 5’-CCTTCTCCAGCATGGGCTC-3’ and 5’-CGTGGGGATAAAGTTGGCACTA-3’, probe, 5’-TGTCAACACACAGGACTTTTGCGCAGAT-3’. The conditions for real-time PCR were 40 cycles at 95°C for 3 s followed by 40 cycles at 60°C for 30 s. The relative mRNA expression levels were normalized to the levels of HPRT mRNA.
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3

RNA Isolation and Real-Time PCR Analysis of VCAM-1 Expression

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Total RNA was isolated from HCFs treated with TNF-α for the indicated time in 10-cm culture dishes with Trizol according to the protocol of the manufacturer. The cDNA obtained from total RNA previously described [33 ]. RT (reverse transcription) of the first-strand cDNA synthesis was performed with 2 μg of total RNA using oligo-dT as primers in a final volume of 20 μl (2 U/μl RNaseOUT, Cat. 10777–019, and 10 U/μl Moloney murine leukemia virus reverse transcriptase (Cat. 28025–013) from Invitrogen (Carlsbad, CA). The reaction was carried out at 37 °C for 60 min.
Real-time PCR using KAPA PROBE FAST ABI Prism® qPCR kit (KK4705, Kapa Biosystems, Wilmington, MA) was performed with the 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA) using primers and probe mixes for VCAM-1 (Forward: WSO_645213_001; Reverse: WSO_645213_002; Probe: WSO_645213_003; Invitrogen) and endogenous GAPDH (Forward: WSO_724786_001; Reverse: WSO_724786_002; Probe: WSO_724786_003) served as an internal control gene (Invitrogen, Carlsbad, CA). Relative gene expression was determined by the ΔΔCt method, where Ct meant threshold cycle [39 (link)]. All experiments were performed in triplicate.
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4

Quantifying NRROS and IL-6 Expression in RBA-1 Cells

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RBA-1 cells were seeded on 10-cm culture dishes and treated with 15d-PGJ2. Total RNA was extracted with TRIzol reagent (Thermo Fisher, Waltham, MA, USA) according to the protocol of the manufacturer. The cDNA obtained from 5 μg total RNA was used to be a template for real-time PCR amplification. Real-time PCR was performed with KAPA PROBE FAST ABI Prism® qPCR kit (KK4705, Kapa Biosystems, Wilmington, MA, USA) and 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) using the sequences of primers as follows:
Rat NRROS:
Forward primer: 5′-CTCATGCTTCAGAACCTCTCCTG-3′
Reverse primer: 5′-CAGAGTCGTCGAGCCTCATG-3′
Probe: 5′-TGGAGGTCGTGTCCTTGGCAAGAA-3′
Rat IL-6:
Forward primer: 5′-CGAAAGTCAACTCCATCTGCC-3′
Reverse primer: 5′-GGCAACTGGCTGGAAGTCTCT-3′
Probe: 5′-TCAGGAACAGCTATGAAGTTTCTCTCCG-3′
Human NRROS:
Forward primer: 5′-TTTTCACTTCCTGACCGTGG-3′
Reverse primer: 5′-CACCAACTTGCAGACTCCTTG-3′
Probe: 5′-AGGAACAGAAGCGGAACAGCCACA-3′
GAPDH:
Forward primer: 5′-AACTTTGGCATCGTGGAAGG-3′
Reverse primer: 5′-GTGGATGCAGGGATGATGTTC-3′
Probe: 5′-TGACCACAGTCCATGCCATCACTGC-3′
Relative gene expression was determined by the ΔΔCt method, where Ct meant the threshold cycle. All experiments were performed in triplicate.
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5

Quantitative Analysis of Heat Stress Genes

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RNA was isolated using an RNeasy kit (QIAGEN). Of each sample, 1 µg of RNA was treated with RQ1 DNaseI (Promega) and reverse transcribed using the iScript cDNA synthesis kit (Bio-Rad Laboratories). Kapa probe fast ABI prism qPCR kit (Kapa Biosystems) was used for the qPCR reaction. The following probes and primers were used: hsp70.1 probe, 5′-FAMTTACACACCTGCTCCAGCTCCTTCCTCTTTAMRA-3′, 5′-GCCGAGAAGGACGAGTTTGA-3′, and 5′-CCTGGTACAGTCCGCTGATGA-3′; hsf2 probe #36 (Universal Probe Library, Roche), 5′-GGAGGAAACCCACACTAACG-3′ and 5′-ATCGTTGCTCATCCAAGACC-3′; gapdh probe, 5′-FAMACCAGGCGCCCAATACGACCAATAMRA-3′, 5′-GTTCGACAGTCAGCCGCATC-3′, and 5′-GGAATTTGCCATGGGTGGA-3′. Relative quantities of hsf2 and hsp70 were normalized against their respective gapdh, and fold inductions were determined after the control was arbitrarily set to a value of 1. The results were analyzed using SDS 2.3 and RQ Manager software (Applied Biosystems). Statistics were calculated using a paired two-tailed Student’s t test for hsp70 mRNA induction and a one-sample t test for the hsf2 mRNA expression.
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6

Quantitative Gene Expression Analysis

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Total RNA were extracted with TRIzol reagent (Thermo Fisher, Waltham, MA, USA) according to the protocol of the manufacturer. The cDNA obtained from 5 μg total RNA was used to be a template for PCR amplification (Torre-Amione et al., 1996 (link)). Real-time PCR was performed with KAPA PROBE FAST ABI Prism® qPCR kit (KK4705, Kapa Biosystems, Wilmington, MA, USA) and 7500 Real-Time PCR System (Applied Biosystems, Foster City, CA, USA) to analyze the amounts of ICAM-1 and GAPDH mRNA. Fold-changes of gene expression were calculated with the ΔΔCt method and all analysis were performed in triplicate (n = 3).
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