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9 protocols using primescript real time pcr kit

1

Baseline Expression of PmMuGST in Shrimp Tissues

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To investigate the basal (control) mRNA level of PmMuGST in various tissues, total RNA was extracted from eight tissues, including hemocytes, hepatopancreas, muscle, heart, ovary, stomach, eyestalk and intestine, from three healthy P. monodon using Trizol regent (Invitrogen, UAS). The amount of PmMuGST mRNA in the different tissues was determined by quantitative real-time PCR (RT-PCR). The RNA samples were analyzed in 1.0 % agarose electrophoresis and quantitated at 260 nm, and all OD260/OD280 ratios were between 1.8 and 2.0. Total RNA (1 μg) was reverse transcribed using the PrimeScript™ Real time PCR Kit (TaKaRa, Otsu, Shiga, Japan) for real-time quantitative RT-PCR analysis. Elongation factor 1-alpha (EF1A) of P. monodon (GenBank accession no. GU136229) was used as an internal control.
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2

Total RNA Extraction from E. sinensis

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TRIzol reagent (Invitrogen) was uesd for the extraction of total RNA from E. sinensis tissue samples, and the first-strand cDNA was synthesised by using the PrimeScript™ real-time PCR kit (Takara, Japan) according to the manufacture’s instruction.
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3

Comprehensive RNA Extraction and Analysis

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Total RNA was extracted from different tissues using an RNA Extraction kit reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The extracted RNA quality and concentration were identified by agarose gel electrophoresis and spectrophotometry, respectively. Total RNA (about 2 μg) was reverse transcribed using the SMART™ cDNA kit (Clontech, Mountain View, CA, USA) for cDNA cloning, and using the Prime ScriptTM RT-PCR Kit (TaKaRa, Dalian, China) for semi-quantitative reverse transcriptase RT-PCR (RT-PCR) analysis or the PrimeScript Real-time PCR Kit (TaKaRa, Dalian, China) for real-time quantitative RT-PCR (qPCR) analysis respectively. Target fragments of HSP60 and HSP10 were obtained from our constructed transcriptome library after using BLAST programs at the National Center for Biotechnology Information [42 (link)]. Based on the target and cloning sequence, all the primers were designed by Primer Premier 5.0 and synthesized by Shanghai Bosun Biotech Co Ltd. (Bosun, Shanghai, China) (Table 1).
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4

Total RNA Extraction and RT-qPCR Analysis

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Total RNA was extracted from different tissues using Trizol reagent (RNA Extraction kit, Invitrogen, CA, USA) according to the manufacturer’s protocol. The concentration and quality of total RNA were estimated by the spectrophotometry (absorbance at 260 nm) and agarose gel electrophoresis, respectively. Total RNA (2 μg) isolated from the gonad was reverse transcribed using the SMART™ cDNA kit (Clontech, CA, USA) for cDNA cloning, and then the PrimeScript Real-time PCR kit (TaKaRa, Toyama, Japan) was used for RT-qPCR experiments, respectively. All the primers used in this study were synthesized by Shanghai Invitrogen Biotech Co Ltd. (Invitrogen, Shanghai, China) and are listed in Table 1.
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5

Caspase-3 Expression via RT-PCR

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Total RNA was extracted using the Blood RNA kit (Omega Bio-tek Inc., Norcross, USA), and reverse transcription-PCR was performed routinely with the PrimeScript real-time-PCR Kit (Takara Bio Inc., Shiga, Japan) for the preparation of CASP-3 cDNA. The primers used for the amplification of the entire CASP-3 coding region (Y1 and Y5) were reported previously [7 (link)]: forward primer (Y1), 5'-AAAGGATCCTTAATAAAGGTATCCATGGAGAACACT-3' (corresponding to -15 to +12 of human CASP-3 mRNA); and reverse primer (Y5), 5'-AAA GAATTCTTAGTGATAAAAATAGAGTTCTTTTGTGAG-3' (+834 to +805 of human CASP-3 mRNA).
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6

Quantitative Real-Time PCR Analysis of Gene Expression

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Total RNA was isolated using TRIZOL reagent (Invitrogen, USA), after which template cDNA for real-time PCR was synthesized using the PrimeScript real time-PCR Kit (Takara Bio, Japan) according to the manufacturer's instructions. Quantitative real-time PCR was conducted using a LightCycler (Roche, Germany) with the SYBR Premix Ex Taq real time-PCR Kit (Takara Bio), LightCycler Fast Start DNA Master SYBR Green I (Takara Bio) and the following primers: β-actin (GenBank accession No. Z70044; forward: GCTGTCCTGTCCCTGTATTCC; reverse: AGCCAAGTCCA GACGACGCAAG), Bax (GenBank accession No. NM_001003011.1; forward: TTGCTTCAGGGTTTCTTCCA; reverse: CGACATTCGCTCCGCTTCTTG), Bcl-2 (GenBank accession No. NM_001002949; forward: CTTCGCCGTGATG TCCAG; reverse: CAGATGCGGGTTCAGATAC) and P53 (GenBank accession No. NM_001003210; forward: AAGA CCTACCCTGGCACCT; reverse: ACCTCGCTCACGAACT CC) according to the manufacturer's protocols. Gene expression was analyzed using the LightCycler software package. Relative gene expression was normalized to that of the housekeeping gene, β-actin, using the protocol described by MW Pfaffl [27 (link)].
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7

Tissue-specific Expression of ALF Genes

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Total RNA was extracted from muscle, hepatopancreas, haemopoietic tissue, gill, and haemocytes and reverse transcribed into cDNA using the Prime-Script™ real-time PCR kit (Takara, Japan) according to the instructions. The spatial distribution of EsALF-1 and EsALF-3 mRNA in the five tissues, and the mRNA expressions of EsALF-1, EsALF-3, EsMy88, EsPelle, and EsTLR1 in haemocytes after immune priming or knockdown of EsTLR1 expression were determined by qRT-PCR with specific primers (Table 1), respectively. The qRT-PCR reactions were conducted with an ABI PRISM 7500 Sequence Detection System (Applied Biosystems) using SYBR green fluorescent (Takara, Japan) according to the instruction. A 267 bp fragment of Esβ-actin (GenBank accession No. HM053699) amplified with the specific primers, Esβ-actin-RT-F and -R (Table 1) was employed as endogenous control. The qRT-PCR reactions operated as follows: 95°C for 10 min, followed by 40 cycles at 95°C for 10 s and 60°C for 45 s. To confirm the specificity of PCR products, the dissociation curve analysis of amplification products was performed at the end of each PCR. The relative mRNA expression level was analyzed by comparative Ct method (2 -△△Ct method) (22 (link)).
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8

Quantifying Gene Expression using qRT-PCR

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Total RNA was isolated from tissue or cells using TRIzol reagent (Invitrogen) and was then reverse‐transcribed into cDNA using PrimeScript real‐time PCR kit (TaKaRa Biotechnology). The real‐time PCR amplification was performed using a SYBR Green PCR Master Mix (TaKaRa) on the ABI 7900 Prism HT (Applied Biosystems). GAPDH was used to internally normalize the expression level of each candidate gene. The relative quantitative comparison between groups was evaluated using the 2−ΔΔCt method.15, 24, 25, 26 Primers for real‐time PCR were as follows: LOC101928477: forward 5′‐CTGCAAGTTTGGGGGTGAAC‐3′, reverse 5′‐ACTGTGGCGAGGTGATATGG‐3′, GAPDH forward 5′‐GGAGCGAGATCCCTCCAAAAT‐3′, reverse 5′‐GGCTGTTGTCATACTTCTCATGG‐3′.
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9

Quantification of Cytokine and Chemokine mRNA

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The RNA of infected cells was extracted using a MiniBEST universal RNA extraction kit (Takara Biotechnology, Dalian, China). cDNA was generated from mRNA using a PrimeScript™ real-time PCR kit with oligo(dT) 12-18 (Takara Biotechnology) according to the manufacturer's protocol. mRNA expression of target genes was carried out using an ABI ViiA™ 7 real-time PCR system (Applied Biosystems, Foster City, CA, USA). The gene expression profiles of cytokines and chemokines were quantified and normalised with β-actin at the respective times. The primers used in these assays have been published previously [16] [17] [18] .
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