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10 protocols using faststart universal sybr premix extaq 2

1

Quantifying Gene Expression in Bone

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The subchondral bones dissected from proximal tibias were pulverized with a pestle and mortar prechilled in liquid nitrogen. The bone particles were homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and the total RNA was harvested following the manufacturer's instructions. cDNA was synthesized from 1 μg of total RNA using a RevertAid First Strand cDNA Synthesis kit (Fermentas, Burlington, Canada). Next, qRT-PCR was performed using a FastStart Universal SYBR Premix ExTaq II (Takara Biotechnology, Japan) on an ABI PRISM 7900HT System (Applied Biosystems, Foster City, CA, USA). Relative gene expression was calculated via the 2–△△CT method and GAPDH was used as the reference for normalization. The primer sequences used for qRT-PCR were as follows: FAK: forward, 5′-GAAGCATTGGGTCGGGAACTA-3′, and reverse, 5′-CTCAATGCAGTTTGGAGGTGC-3'; GAPDH: forward, 5′-TGTCGTGGAGTCTACTGGTG-3′; and reverse, 5′-GCATTGCTGACAATCTTGAG-3′.
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2

Total RNA Extraction and qRT-PCR Analysis

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Total RNA was extracted using the TRIzol Reagent (Life Technologies Inc., Carlsbad, CA, USA), which was maintained at −80°C refrigerator for preservation. RNA was used for cDNA synthesis with the Superscript III Reverse Transcription Reagent (Life Technologies). MiRcute miRNA isolation kit (Tiangen, China) was used for miRNA extraction. Qiagen miScript Reverse Transcription kit (Qiagen, Germany) was used for reverse transcribe. Following the formula recommended by FastStart Universal SYBR Premix Ex Taq™ II (Takara, Japan), the formula containing 14 μL 2 × SYBER Green master mix, 1 μL forward primer (10 μM), reverse primer 1 μL (10 μM), 3 μL cDNA template, 6 μL ddH2O was set up. Later, the reaction system was reacted in Bio-Rad IQ5 thermocycler (Bio-Rad, CA, USA) following the procedures: 90 s at 95°C for start, 25 s at 95°C, 20 s at 65°C, 30 s at 72°C for the amplification. Forty cycles were performed. GAPDH and U6 were used as controls.
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3

qRT-PCR Analysis of Worm Gene Expression

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Total RNA was isolated using TRIzol reagent (Invitrogen) in N2, VP303, TU3401, and VP303; N-daf-2 KO worms under the indicated RNAi conditions. The extracted total RNA was reverse-transcribed into single-stranded cDNA using the ReverTra Ace qPCR RT Master Mix with gDNA Remover kit (TOYOBO) according to the manufacturer’s protocol. Quantitative RT-PCR was performed with an ABI 7300 Real-Time PCR system (Applied Biosystems) using FastStart Universal SYBR Premix Ex TaqTM II (TAKARA). The relative mRNA levels were determined using the ΔΔCT method. The relative mRNA levels were normalized to that of act-1, a C. elegans housekeeping gene.
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4

Quantifying Osteogenic Gene Expression in BMSCs

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We isolated total RNA from BMSCs by TRIzol reagent (Life Technologies, USA) and synthesized complementary DNAs (cDNAs) from total RNA. Then, we performed quantitative reverse transcriptase PCR (qRT-PCR) by FastStart Universal SYBR Premix ExTaqTM II (Takara Biotechnology, Japan) on an ABI Prism 7900 HT Sequence detection system (Applied Biosystems, USA). We used 100 μl RNA in RT-PCR experiments. The reaction conditions were as follows: 95°C, 30 s; 95°C, 10 s; 60–65°C, 10 s; for 40 cycles. The primer sequences used for qRT-PCR were as follows: Alp: forward, 5′-CCA ACT CTT TTG TGC CAG AGA-3′ and reverse, 5′-GGC TAC ATT GGT GTT GAG CTT TT-3′; Ocn: forward, 5′- CTG CGC TCT GTC TCT CTG AC-3′ and reverse, 5′- TTA AGC TCA CAC TGC TCC CG-3′; OPG: forward, 5′- AGT GTG AGG AAG GGC GTT AC-3′ and reverse, 5′-AAT GTG CTG CAG TTC GTG TG-3′; Runx2: forward, 5′-AAA TGC CTC CGC TGT TAT GAA-3′ and reverse, 5′-GCT CCG GCC CAC AAA TCT-3′.
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5

RNA Isolation and qPCR Analysis

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Total RNA was isolated using TRIzol Reagent (Takara) according to the manufacturer's instructions. The concentration of RNA was determined by measuring the optical density at wavelengths of 260 nm and 280 nm. 1 μg of the total RNA was used to generate cDNA with the First Strand cDNA Synthesis kit (Bimake). Then, qPCR was performed using FastStart Universal SYBR Premix ExTaqTM II (Takara Biotechnology) on an ABI PRISM® 7900HT System (Applied Biosystems). The relative gene expression was analysed by the relative standard curve method (2−ΔΔCT) with Gapdh as the reference. The primers used for qPCR are listed in Table S1.
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6

Quantitative Real-Time PCR Protocol

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Total RNA of cultured cells was extracted using TRIzol reagent (Thermo Scientific) following the manufacturer’s instructions. One microgram of total RNA was then reverse-transcribed into complementary DNA using All-in-One cDNA Synthesis SuperMix (Biotool, USA). qRT‒PCR was performed with FastStart Universal SYBR Premix ExTaqTM II (TaKaRa Biotechnology, Japan) on an FTC-3000 real-time PCR system (Funglyn Biotech, Canada). Relative expression was calculated for each gene by the 2−ΔΔCT method, and GAPDH amplification was used as an internal normalization. Sequences of the primers used for each gene are listed in Supplementary Table 1.
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7

Quantifying Cytokine Expression in Cyanobacteria Treatments

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TRIzol Reagent (Invitrogen) was used to extract total RNA from cells treated with S. elongatus PCC 7942 (106 cells/mL), S. elongatus-EVs (100 μg/mL) or an equal volume of PBS for 24 h. cDNA was synthesized using 1 μg of total RNA with a RevertAid First Strand cDNA Synthesis kit (Fermentas, Burlington, Canada) and then amplified on an ABI PRISM® 7900HT System (Applied Biosystems, Foster City, USA) with FastStart Universal SYBR Premix ExTaqTM II (Takara Biotechnology, Japan). The 2-△△CT method was adopted to calculate the relative gene expression and GAPDH was used as an internal control gene to normalize the expression of target gene. Primer sequences used for qRT-PCR analysis were as follows: IL-6: forward, 5'-TAGTCCTTCCTACCCCAATTTCC-3', and reverse, 5'-TTGGTCCTTAGCCACTCCTTC-3'; Gapdh: forward, 5'-CACCATGGAGAAGGCCGGGG-3', and reverse, 5'-GACGGACACATTGGGGGTAG-3'.
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8

Quantitative Analysis of Bone Tissue Gene Expression

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Total RNA from bone tissues or cultured cells was isolated using TRIzol reagent (Life Technologies, USA) and complementary DNAs (cDNAs) were synthesized from 1 μg of total RNA using a high-capacity cDNA reverse transcription kit (Applied Biosystems, USA). Then, quantitative reverse transcriptase PCR (qRT-PCR) was performed using FastStart Universal SYBR Premix ExTaqTM II (Takara Biotechnology, Japan) on an ABI Prism 7900 HT Sequence detection system (Applied Biosystems, USA). The primers for mRNAs were purchased from Sangon Biotech Co., Ltd, Shanghai. The primer sequences used for qRT-PCR were as follows: Alp: forward, 5′-CCA ACT CTT TTG TGC CAG AGA-3′ and reverse, 5′-GGC TAC ATT GGT GTT GAG CTT TT-3′; BGLAP: forward, 5′-CTG ACC TCA CAG ATG CCA AGC-3′ and reverse, 5′-TGG TCT GAT AGC TCG TCA CAA G-3′; HDAC7: forward, 5′-TGA AGA ATG GCT TTG CTG TG-3′ and reverse, 5′-CAC TGG GGT CCT GGT AGA AA-3′; mmu-miR-143–3p: forward, 5′-GGG GTG AGA TGA AGC ACT G-3′ and reverse, 5′-CAG TGC GTG TCG TGG AGT-3′; GADPH: forward, 5′-CAC CAT GGA GAA GGC CGG GG-3′ and reverse, 5′-GAC GGA CAC ATT GGG GGT AG-3′.
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9

RNA Extraction and qRT-PCR Analysis

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The subchondral bones dissected from the proximal tibias, chilled in liquid nitrogen, were cut into pieces. We used TRIzol reagent (Invitrogen, Carlsbad, CA) for the homogenization of the specimens, and then, the total RNA was harvested. One milligram of total RNA was employed to synthesize cDNA using a cDNA Synthesis kit (Fermentas, Burlington, Canada). After that, FastStart Universal SYBR Premix ExTaqTM II (TaKaRa Biotechnology, Japan) was employed to conduct qRT‒PCR. The 2−△△CT approach was employed to measure relative gene expression.
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10

Quantitative RT-PCR for Gene Expression

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Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA) and cDNA was synthesized from 1 μg of total RNA by using the RevertAid First Strand cDNA Synthesis kit (Fermentas, Burlington, Canada). Next, qRT-PCR was performed using FastStart Universal SYBR Premix ExTaqTM II (Takara Biotechnology, Japan) on an ABI PRISM® 7900HT System (Applied Biosystems, Foster City, USA). Relative gene expression was calculated by the 2-△△CT method and GAPDH was used as reference for normalization. Primer sequences used for qRT-PCR were as follows: Atp6v0d2: forward, 5'-AGCAAAGAAGACAGGGAG-3', and reverse, 5'-CAGCGTCAAACAAAGG-3'; Ctsk: forward, 5'-GCGGCATTACCAACAT-3', and reverse, 5'-CTGGAAGCACCAACGA-3'; Pdgf-bb: forward, 5'-CCTCGGCCTGTGACTAGAAG-3', and reverse, 5'-CCTTGTCATGGGTGTGCTTA-3'; Gapdh: forward, 5'-CACCATGGAGAAGGCCGGGG-3', and reverse, 5'-GACGGACACATTGGGGGTAG-3'.
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