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13 protocols using sybr premix ex taqtm 2 pcr kit

1

Quantitative Gene Expression Analysis

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Total RNA was extracted using the Trizol reagent (Invitrogen) according to the manufacturer's protocol. RNA was reverse transcribed into complementary DNA (cDNA) with an RNA reverse transcription kit (Takara) following the manufacturer's protocol. The cDNA was amplified using primers (sequences and their accession number to GenBank are listed in Table S1) specific for alkaline phosphatase (ALP), runt‐related transcription factor 2 (RUNX2), bone sialoprotein (BSP), osteocalcin (OCN), receptor activator of nuclear factor‐κB ligand (RANKL), osteoprotegerin (OPG), α7 nAChR (CHRNA7), GSK3B and β‐actin (ACTB).
Quantitative PCR was performed in a volume of 20 μL using SYBR Premix Ex TaqTM II PCR kit (Takara). PCR conditions were selected according to the suggested protocol for the CFX Connect Real‐Time PCR Detection System (Bio‐Rad). β‐actin was used as an internal reference gene, and the 2−ΔΔCt method was used to calculate expression of target genes between the experimental group and control group.
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2

Quantitative RT-PCR for MTERFD1 Expression

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Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) per the manufacturer's protocol. The cDNA was synthesized by reverse transcribing the total RNA using the PrimeScriptTM RT reagent kit with gDNA Eraser (TaKaRa, Shiga, Japan) as per the product manual. qRT-PCR was performed using the SYBR Premix Ex TaqTM II PCR Kit (TaKaRa, Shiga, Japan) and the standard protocol of the Applied Biosystem 7500 Fast Real-Time PCR System (ABI, Foster City, CA, USA). The primers used in the qRT-PCR were GAPDH (5'-CCATGTTCGTCATGGGTGTGAACCA-3' and 5'-GCCAGTAGAGGCAGGGATGATGTTC-3') and MTERFD1 (5'- AGGCTGCTAACTGGAAGTCTGG-3' and 5'-ATGATGTGGTGGGGAATGCTCA-3'). Relative mRNA levels of MTERFD1 were normalized to the GAPDH reference gene expression and calculated via the 2-△△CT method.
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3

Transcriptional Profiling of Bronchial Epithelial Cells

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Total RNA was extracted from bronchial epithelial cells by using Trizol reagent (Invitrogen, CA, USA). Extracted RNA was reverse transcribed to cDNA using a reverse transcription kit (Takara, China). TRPC1 forward, 5’-GAAGATTTTGGGAAATTTCTGG −3’, TRPC1 reverse, 5’-CTTATCCTCATGTTTGCTAT-3’, TGF-β1 forward,5-CGACTCGCCAGAGTGGTTAT-3′, TGF-β1 reverse, 5’-CAGTAGTGAACCCGTTGACCT-3’, MMP-9 forward, 5’-CAACTCTGGAGGTTCGAC-3’, MMP-9 reverse, 5’-CATTCACGCGCCAGTAGCCG-3’, GAPDH forward 5’-AATCCCATCATCACCATCTTCCA-3’, GAPDH reverse 5’-CCTGCTTCACCACCTTCTTGAGG-3’. RT-qPCR was performed using the SYBR Premix Ex TaqTM II PCR kit (Takara, China). The reaction condition was incubated at 95°C for 3 min, followed by 40 cycles of denaturation at 94°C for 15 sec, annealing at 55°C for 30 sec, and then elongation at 72°C for 30 sec. GAPDH was selected for normalization. The relative expression of TRPC1 was calculated by using the 2−ΔΔCt.
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4

Quantifying Mouse PMCA4 Expression via RT-qPCR

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Total RNA was extracted from mouse testes using TRIzol (Thermo Fisher Scientific, Inc.) and cDNA synthesis was performed using the PrimeScript RT Master Mix kit (Takara Bio, Inc.) according to the manufacturer's protocol. RT-qPCR reactions were performed with the SYBR® Premix EX TaqTMII PCR kit (Takara Bio, Inc.), with primers specific for mouse PMCA4 (forward, 5′-CTGAGGGAATGGACGAGAT-3′ and reverse, 5′-CAACTGCTGCGGAATAGGA-3′; product size, 204 bp), with GAPDH (forward, 5′-AGTGGCAAAGTGGAGATT-3′; and reverse, 5′-GTGGAGTCATACTCCAACA-3′; product size, 116 bp) used as the endogenous control. The annealing temperature was 60°C, with 40 cycles. Data were calculated using 2−ΔΔCq method (12 (link)).
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5

Quantification of MCT1 and MCT4 Expressions

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Total RNA was extracted using the Trizol reagent (Invitrogen, USA) as per the instruction of the manufacturer’s manual. The extracted RNA was quantified using a NanoDrop device (ThermoFisher Scientific) and stored at − 80 °C pending subsequent analysis. The PrimeScript RT Reagent Kit (Takara, Japan) was used for reverse transcription of total RNA into complementary DNA (cDNA). The expression level of MCT1 and MCT4 were assessed by RT-qPCR using the SYBR®premix ExTaqTM II PCR Kit (Takara, Japan). The primers were synthesized by Sangon, Shanghai, China, and the sequences are as follows:

MCT1, Forward, 5′-TGGATGGAGAGGAAGCTTTCTAAT-3′.

Reverse, 5′-CACACCAGATTTTCCAGCTTTC-3′.

MCT4, Forward, 5′-CACGGCATCGTCACCAACT-3′.

Reverse, 5′-ACAGCCTGGATAGCAACGTACAT-3′.

GAPDH, Forward, 5′-CGGAGTCAACGGATTTGGTCGTAT-3′.

Reverse, 5′-AGCCTTCTCCATGGTGGTGAAGAC-3′.

GAPDH was the housekeeping gene used for the control. The experiments were performed 3 times and triplicated wells were used in each group in one experiment. The reaction conditions for PCR were set as follows: pre-denaturation at 95 °C for 30 s, 45 cycles of denaturation at 95 °C for 5 s, and annealing at 58 °C for 34 s. The 7500 Real-Time PCR System (Thermo Fisher Scientific) was used to perform the assay. The 2−ΔΔCt method was used to calculate the expression of the target gene between the experimental group and the control group.
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6

Quantifying lncRNA NEAT1 Expression

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RNA was reverse transcribed into cDNA using the PrimeScript RT Master kit (Takara, RR037A). RT-qPCR was performed with the SYBR® Premix EX TaqTM II PCR Kit (Takara, DRR041A) following the manufacturer’s instructions on the Roche Lightcycler 480 Real-Time PCR System. Data were calculated according to the Applied Biosystems comparative Ct method. Primers used for LncRNA NEAT1 and GAPDH qRT-PCR were as follows:
LncRNA NEAT1-Forward: 5′-GGA​TGA​GGC​CTG​GTC​TTG​T-3’.
LncRNA NEAT1-Reverse: 5′-GAG​AAA​AGT​CCA​AAA​GGA​GCA​C-3’.
GAPDH-Forward: 5′-ACA​ACT​TTG​GTA​TCG​TGG​AAG​G-3’.
GAPDH-Reverse:5′-GCCATCACGCCACAGTTTC-3’.
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7

Quantification of miR-1296 and ABL2 Expression

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Total RNA was extracted from the cell lines or tumor samples using the TRIzol reagent (Thermo Fisher Scientific Inc.) according to the manufacturer’s instruction. RNA concentration was monitored with the NanoDrop (Thermo Fisher Scientific Inc.). Reverse transcription was performed using the Hairpin-itTM miRNA quantitative detection kit (GenePharma, Shanghai, China). qPCR was conducted on the ABI7500 platform with the SYBR Premix Ex TaqTM II PCR Kit (Takara, Dalian, China) following the manufacturer’s protocol. The primers of miR-1296 (F: 5′-GTTAGGGCCCTGGCTCC-3′ and R: 5′-CAGTGCGTGTCGTGGAGT-3′), ABL2 (F: 5′-GTGATGAGACTACTGCAGCATCC-3′ and R: 5′-CGGTTACCGTGTCGTCCATGAT-3′), GAPDH (F: 5′-CCATGTTCGTCATGGGTGTGAACCA-3′ and R: 5′-GCCAGTAGAGGCAGGGATGATGTTC-3′) and U6 RNA (F: 5′-GCTTCGGCAGCACATATACTAAAAT-3′ and R: 5′-CGCTTCAGAATTTGCGTGTCAT-3′) were designed and synthesized by GenePharma (Shanghai, China). U6 RNA and GAPDH was detected as the internal reference of miR-1296 and ABL2, respectively. The relative expression of miR-1296 was analyzed with the 2-ΔΔCq method.
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8

miRNA Expression Analysis by qRT-PCR

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Total RNA was extracted with TRIzol reagent (Invitrogen) and then reverse transcribed to cDNA according to the protocol of the miRcute miRNA First-strand cDNA synthesis kit (Beijing Tiangen Biotechnology, Ltd). cDNA was subjected to real-time PCR using a SYBR premix Ex TaqTM II PCR kit (Takara, Dalian, Liaoning Province, China) with the ABI 7500 real-time PCR instrument. Quantitation of miR-519d was normalized to U6, and LEP was normalized to GAPDH. The primer sequences are listed in Table S1. Results were calculated by 2−ΔΔCT method.
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9

Quantification of lncRNA SSTR5-AS1 Expression

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The total RNA from the cultivated cells was extracted with Trizol reagent (Invitrogen, California, USA) in accordance with the instructions provided by the manufacturer. In the second step, 2 μg of total RNA was subjected to reverse transcription utilizing a PrimeScript™ RT reagent kit with gDNA Eraser (Takara, Dalian, Niaoning, China) in an overall volume of 20 L in accordance with the procedure provided by the manufacturer. After that, a real-time quantitative polymerase chain reaction (qRT-PCR) was performed with the SYBR Premix Ex TaqTM II PCR Kit (Takara, Otsu, Shiga, Japan) by carefully adhering to the instrument that was provided by the manufacturer. Results were normalized to the content of GAPDH. The results of each experiment were recorded three times. The 2ΔΔCt method was used to represent the fold-change values of lncRNA expression. Primers used for RT-RCR are presented as follows: SSTR5-AS1-F: 5′-ACTACAGGTGCCATCAGACC-3′, SSTR5-AS1-R: 5′-AGCCTGCCATCCTAACACTT-3′; GAPDH-F: F: 5′-AGGTGAAGGTCGGAGTCAACG-3′, GAPDH-R: R: 5′-AGGGGTCATTGATGGCAACA-3′.
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10

RNA Extraction and RT-qPCR Analysis

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Total RNA from WT and SCARKO mice was prepared with Trizol reagent according to the manufacturer’s instructions. Then RNA was reverse transcribed into cDNA using the PrimeScript RT Master kit (Takara, RR037A). RT-qPCR was performed with the SYBR® Premix EX TaqTM II PCR Kit (Takara, DRR041A) following the manufacturer’s instructions on the Roche Lightcycler 480 Real-Time PCR System. Data were calculated according to the Applied Biosystems comparative Ct method.
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