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11 protocols using primescript rt master mix

1

RNA Isolation and RT-qPCR Analysis of Periodontal Tissue

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Total RNA was purified from periodontal tissue with TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and cDNA was generated using PrimeScript RT Master Mix (Toyobo Co, Ltd, Osaka, Japan). The cells isolated by FACS were lysed, and reverse transcription was performed using a SYBR™ Green Fast Advanced Cells-to-CT™ Kit (Thermo Fisher Scientific, Inc., Waltham, MA, USA). Gene expression levels were measured by RT-qPCR using a BioRad CFX96TM Detection System (Roche, Sweden) and SYBR PCR Master Mix (Roche, Indianapolis, IN, USA). The primers used in this experiment are shown in Supplementary Table 2.
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2

Quantitative RNA Expression Analysis

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Total RNA was isolated using TRIzol (Thermo Fisher), and then 1 μg RNA was reverse transcribed using Prime Script RT Master Mix (Toyobo). Quantitative PCR was performed using the Power SYBR green PCR Master Mix (Toyobo). The amounts of transcript were normalized to those of glyceraldehyde-3-phosphate dehydrogenase (GAPDH).
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3

Quantifying Gene and miRNA Expression

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Total RNA was extracted from periodontal tissue and cells with TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and cDNA was generated with PrimeScript RT Master Mix (Toyobo Co, Ltd, Osaka, Japan). The expression level of genes was measured by qPCR in a Bio-Rad CFX96™ Detection System (Roche, Sweden) with SYBR PCR Master Mix (Roche, Indianapolis, IN, USA). Small RNA was extracted from cells with an miRNA isolation kit (Qiagen, Hilden, Germany), and cDNA was generated with an miRNA reverse transcription kit (Shenggong, Shanghai, China). The expression level of miRNAs was measured by qPCR in a Bio-Rad CFX96™ Detection System with SYBR PCR Master Mix. U6 was used as the internal reference. The primers used are shown in Supplementary Table S1.
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4

Quantifying TMPRSS4 Gene Expression

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Total RNA was isolated using the TRIzol agent (Invitrogen, Carlsbad, CA, USA) and RNA samples (1 μg) were reverse transcripted to cDNA using PrimeScript RT Master Mix (538100; Toyobo, Osaka, Japan). The qPCR was performed using SYBR-Green PCR Master Mix (15153900; Roche, Indianapolis, IN, USA) on the Applied Biosystems 7900HT Real-time PCR system. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) mRNA was used as an internal control for each sample, and the expression of each sample was normalized to GAPDH mRNA. Primers used were as follows: TMPRSS4 forward, 5′-CCGATGTGTTC AACTGGAAG-3′ and reverse, 5′-GAGAAAGTGAGTGG GAACTG-3′; GAPDH forward, 5′-GCACCGTCAAGGCTG AGAAC-3′ and reverse, 5′-TGGTGAAGACGCCAGTGGA-3′. After denaturation for 10 min at 95°C, the reaction was continued for 40 cycles at 94°C for 10 sec, 60 or 62°C for 20 sec and 72°C for 20 sec. The relative expression of each miRNA was calculated using the 2−ΔΔCt method.
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5

Quantitative RT-PCR Analysis of Gene Expression

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Total RNA was extracted by Trizol reagent (Invitrogen, USA), and the cDNA was synthesized with PrimeScript™ RT Master Mix (Toyobo Life Science, Japan). In brief, 1 μg total RNA was used to reverse transcribe 20 μL cDNA, and 1.5 μL of cDNA was used for each qPCR. RT-qPCR experiments were performed using the SYBR-Green Premix Ex Taq kit (Takara, Japan) and were assessed by Roche Lightcycler 480 Real-Time PCR System. The following cycling conditions were used for qPCR: preheat for 1 cycle at 94°C for 30 sec, amplification for 40 cycles at 94°C for 5 s, 60°C for 10 s and cooling to 50°C for 30 s. The primers were listed as follows: PLA2G6, forward primer: 5’-TTTGGCCGCCTGGTCAATAC-3’ and reverse primer: 5’-CTCCCGAACTCGGTCACTC-3’; GAPDH, forward primer: 5’-CATCTTCTTTTGCGTCGCCA-3’ and reverse primer: 5’-TTAAAAGCAGCCCTGGTGACC-3’. The relative expressions of mRNAs were evaluated by the 2−ΔΔCq method. Three independent experiments were performed.
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6

Quantifying Gene Expression via RT-qPCR

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Total RNA extraction from the cells was carried out utilizing Trizol (Invitrogen). Subsequently, cDNA was synthesized from 1 μg of total RNA employing the PrimeScript RT Master Mix (TOYOBO, Japan). Reverse transcription quantitative PCR (RT-qPCR) was conducted using the Fast SYBR Green Master Mix (TOYOBO, Japan) on a 7500 Fast Real-Time PCR system. Quantification of gene expression was performed using the delta-delta CT method, with target gene expression levels being normalized to β-actin expression levels. The primer sequences used are provided below:
ICAM-1, ATCTGTGTCCCCCCTCAAAAGTC (forward), CCATCAGGGCAGTTTGAATAGC (reverse); IL-6, 5’-ACTCACCTCTTCAGAACGAATTG-3’ (forward), 5′-CCATCTTTGGAAGGTTCAGGTTG-3’ (reverse); Cx43, 5′-TCTGAGTGCCTGAACTTGC-3’ (forward), 5′-ACTGACAGCCACACCTTCC-3’ (reverse); β-actin, 5’-ATCACCATTGGCAATGAGCG-3’ (forward), 5’-TTGAAGGTAGTTTCGTGGAT-3’ (reverse).
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7

RNA extraction and RT-qPCR protocol

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TRIzol® reagent (Thermo Fisher Scientific, Inc) was used for RNA extraction when cell confluence was 70-80%. Prime Script RT Master Mix (Toyobo Life Science) was used for mRNA reverse transcription. Reverse transcription of miRNA was performed using miRNA first-strand cDNA synthesis (tailing method) kit (Sangon Biotech, China). RT-qPCR was performed using SYBR Premix EX Taq TMII (Toyobo Life Science). RNA extraction, cDNA synthesis and qPCR were performed according to the manufacturer's protocols. PCR cycle conditions: Denaturation (95°C, 30 sec); annealing (95°C, 5 sec) and extension (60°C, 30 sec) for 40 cycles. Quantification method was ΔCt=Ct (target gene)-Ct (internal reference gene), ΔΔCt=ΔCt (experiment group)-ΔCt (control group) and final results were shown as 2ΔΔCq (12 (link)). These experiments were repeated at least 3 times. The internal references for mRNA and miRNA extracted from cells were GAPDH and U6, respectively. However, miRNAs extracted from exosomes used miR16-5p as an internal reference. The primer sequences for RT-qPCR are given in Table SI.
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8

Mouse Brain and Astrocyte RNA Profiling

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Previously isolated RNA from whole mouse brain or primary astrocytes was reverse transcribed with PrimeScript RT Master Mix (Toyobo), according to the manufacturer’s protocol. cDNA was run on a two-step PCR using TB Green™ Premix Ex Taq™ (Toyobo). The cycling conditions were as follows: pre-denaturation at 95 °C for 30 s, followed by 40 cycles of denaturation at 95 °C for 5 s and extension at 60 °C for 30 s. Specific primers for the genes of Hrh1 (5′ → 3′ sense: TCACTCCAGGCCTCACATG; antisense: CAAAGTTCTCATCCCAAGTTTCCA, 95 bp), Cre recombinase (Cre) (5′ → 3′ sense: CGACCAGGTTCGTTCACTCA; antisense: CAGCGTTTTCGTTCTGCCAA, 186 bp), and glyceraldehyde 3-phosphate dehydrogenase (Gapdh) (5′ → 3′ sense: AGAACATCATCCCTGCATCC; antisense: CACATTGGGGTAGGAACAC, 91 bp) were used for amplification.
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9

Quantitative PCR analysis of GNAI2 gene

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Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA) was used to extract the total cellular RNA, which was later prepared in cDNA by reverse transcription using the PrimeScript RT Master Mix (538100; Toyobo, Osaka, Japan). Thereafter, the Applied Biosystems 7900HT real-time PCR system (Foster City, CA, USA) was used for qPCR through SYBR-Green PCR Master Mix (15153900; Roche, Basel, Switzerland). The cDNA concentration was adjusted to 30 ng/μL. Fluorescence qPCR was performed as follows: 2 min at 95°C, then 15 s at 95°C, and 30 s at 60–68°C for 40 cycles, with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) being the endogenous reference gene. Fold changes (FCs) in the gene level were determined using the 2-ΔCt approach. All assays were carried out in triplicate. The primer sequences for GNAI2 were forward primer: TACCGGGCGGTTGTCTACA and reverse primer: GGGTCGGCAAAGTCGATCTG.
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10

Analysis of ER Stress Markers in HGECs

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HGECs were suspended in 1 mL of TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and stored at - 80°C.
Total RNA was puri ed using TRIzol reagent following the manufacturer's instructions and quanti ed with a Nanodrop 2000. cDNA was synthesized from 500 ng of total RNA using Prime Script RT Master Mix (Toyobo Co, Ltd, Osaka, Japan). Real-time PCR was performed in a 96-well optical reaction plate using SYBR PCR Master Mix (Roche, Indianapolis, IN, USA). mRNA expression was assayed on a Bio-Rad CFX96 detection system (Roche, Sweden). Details of the RT-qPCR primers used in this experiment are shown in Table 1. Relative SERPINH1, GRP78, IRE1, TRAF2, NLRP3, IL-1β, XBP1-s and XBP1-u expression was quanti ed with the 2-ΔΔCt method using GAPDH expression as an endogenous control.
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