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Thermal cycler cfx6 system

Manufactured by Bio-Rad
Sourced in United States

The Thermal Cycler CFX6 System is a real-time PCR instrument designed for gene expression analysis, genotyping, and other molecular biology applications. The system features a 96-well block format and can perform up to 6 independent real-time PCR reactions simultaneously.

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16 protocols using thermal cycler cfx6 system

1

Quantifying circPVT1 and miR-137 Expression

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According to the standard protocol, total RNA from tissues and cells was first extracted by using the TRIzol reagent (Invitrogen). After quantification with NanoDrop (NanoDrop Technologies, Wilmington, WI, USA), the extracted RNAs were reverse-transcribed to the first-strand complementary DNA (cDNA) using the PrimeScript™ RT Master Mix (TaKaRa, Dalian, China). With the help of the Thermal Cycler CFX6 System (Bio-Rad, California, USA), RT-qPCR was carried out using an SYBR Green PCR Kit (TaKaRa). Then, the obtained data were calculated by the 2ΔΔCt method, normalized to glyceraldehyde 3-phosphate dehydrogenase (GAPDH for circPVT1 and TRIAP1) and U6 (for miR-137). The primers are showed in Table 1.
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2

RNA Extraction and qPCR Analysis

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RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) protocol. cDNA was obtained according to the protocol of the Prime Script™ RT Master Mix Kit (Takara, Kusatsu, Japan), and q-PCR assay was performed using SYBR Premix Ex Taq™II (Takara, Kusatsu, Japan) on a Thermal Cycler CFX6 System (Bio-Rad, Hercules, CA, USA). The relative gene expression levels were assessed using the 2−ΔΔCt method.
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3

Quantification of Circular RNA, mRNA, and miRNA

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Total RNA was isolated using the RNA extraction kit (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s protocols, and then 500 μg of total RNA was reverse-transcribed into complementary DNA (cDNA) using the PrimeScript™ RT reagent kit (Takara, Dalian, China). For the detection of miR-377-3p expression, the Hairpin-it TM miRNAs qPCR Quantitation Kit (Genepharma, Shanghai, China) was used. The RT-qPCR assay was conducted using SYBR Green Real-Time PCR Master Mix (Applied Biosystems, Carlsbad, CA, USA) on a Thermal Cycler CFX6 System (Bio-Rad, Hercules, CA, USA) and quantified with the 2−ΔΔCt method. The expression levels of circ-CFH and RNF38 were normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH), while the expression level of miR-377-3p was normalized to small nuclear RNA U6. The sequences of primers are listed in Table 2.
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4

RNA Extraction and qRT-PCR Quantification

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All RNAs were extracted according to the instruction of Trizol Reagent (Invitrogen). Then the cDNAs were synthesized following the protocol of PrimeScript™ RT Master Mix (Takara). Quantitative real‐time PCR was conducted using SYBR Premix Ex Taq™ II (Takara) on Thermal Cycler CFX6 System (BioRad). The relative expression of genes was calculated by the 2−ΔΔCt formula. U6 and β‐actin were used as internal reference. The primers involved were presented in Table 2.
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5

Extraction and Quantification of RNA

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The extraction of total RNA from tissues and cells was implemented using Trizol reagent (Takara, Dalian, China) in accordance with the operation manual. Reverse transcription of lncRNA/mRNA and miRNA were conducted using a SuperScript Reverse Transcriptase Kit (Vazyme, Nanjing, China) and Poly (A) Tailing Kit (Thermo Fisher Scientific, Waltham, MA, USA), respectively. Quantification of RNA was performed using SYBR Fast qPCR Mix (Thermo Fisher Scientific) in the Thermal Cycler CFX6 System (Bio-Rad, Hercules, CA, USA). The internal expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and endogenous small nuclear RNA U6 was used for the normalization of detected RNA using the 2−ΔΔCt method, and the PCR program was: at 95°C for 10 min, followed by 95°C for 15 s and 60°C for 1 min for 40 cycles.
The sequences of primers were:
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6

Quantitative RT-PCR Analysis of Gene Expression

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Total RNA was extracted from tissues and cultured cells using TRIzol reagent (Invitrogen, CA, USA) following the supplier’s directions. 1 mg of total RNA was converted to complementary DNA (cDNA) with specific primers in line with the protocol of a PrimeScript RT master mix kit (Takara, Tokyo, Japan). Quantitative real-time PCR was performed using a SYBR Green PCR kit (Takara) on Thermal Cycler CFX6 system (Bio-Rad, CA, USA). The amplification parameters were as follows: denaturation at 95°C for 10 min, followed by 40 cycles of denaturation at 95°C for 30 s, annealing at 60°C for 30 s, and extension at 72°C for 1 min. The relative RNA expressions were calculated by the 2−ΔΔCt method, normalizing to GAPDH or U6. A quantitative real-time PCR assay was performed at least three times.
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7

Quantitative Real-Time PCR Analysis of Gene Expression

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The total RNA was extracted from tissues or cultured cells according to the instruction of Trizol Reagent (Invitrogen). Then, the cDNAs were synthesized following the protocol of PrimeScript™ RT Master Mix (Takara). Quantitative real‐time PCR was conducted using SYBR Premix Ex TaqTM II (Takara) on Thermal Cycler CFX6 System (BioRad). β‐actin was used as internal reference. The relative expression of genes was calculated using the 2−ΔΔCt method. The primers used in this study were presented in Supplementary Table 1.
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8

Quantification of miR-199a-5p Expression

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Th overall RNA from the tissues and cells was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and then subjected to reverse transcription using the PrimeScript RT Reagent Kit (TaKaRa, Tokyo, Japan). The complementary RNA underwent a qRT-PCR analysis using the Thermal Cycler CFX6 System (Bio-Rad, Hercules, CA, USA), and the SYBR Green PCR Kit (TaKaRa). After normalizing miR-199a-5p to U6, the gene level was measured using the 2-ΔΔCt method.
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9

Quantitative Evaluation of RNA Expression

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Total RNA was isolated using TriQuick Reagent (Solarbio) in accordance with the producer’s procedures. For lncRNA/mRNA, RNA was used to synthesize complementary DNA (cDNA) with a cDNA Reverse Transcription kit (Bio-Rad, Hercules, CA, USA). The expression levels of lncRNA/mRNA were evaluated using Quantitect SYBR Green Kit (Qiagen, Hilden, Germany) based on the 2−ΔΔCt method, with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as an internal control. For miR-98-5p, cDNA was synthesized and amplified using miScript II RT kit (Qiagen) under Thermal Cycler CFX6 System (Bio-Rad). The expression level of miR-98-5p was standardized to endogenous small nuclear RNA U6.
The sequences of primers used were listed:

α-SMA (Forward-5ʹ-GTCCACCGCAAATGCTTCTAA-3ʹ; Reverse-5ʹ- AAAACACATTAACGAGTCAG-3ʹ);

SM22-α (Forward-5ʹ-TGATTCTGAGCAAGCTGGT-3ʹ; Reverse-5ʹ- TGCCTTCAAAGAGGTCAAC -3ʹ);

XIST (Forward-5ʹ-CTCTCCATTGGGTTCAC-3ʹ; Reverse-5ʹ- GCGGCAGGTCTTAAGAGATGAG -3ʹ);

miR-98-5p (Forward-5ʹ-GCCGAGTGAGGUAGTAAGTTG-3ʹ; Reverse-5ʹ- CTCAACTGGTGTCGTGGA-3ʹ);

PAPPA (Forward-5ʹ-ACAAAGACCCACGCTACTTTTT-3ʹ; Reverse-5ʹ- CATGAACTGCCCATCATAGGTG-3ʹ);

GAPDH (Forward-5ʹ-TCCCATCACCATCTTCCAGG-3ʹ; Reverse-5ʹ- GATGACCCTTTTGGCTCCC-3ʹ);

U6 (Forward-5ʹ-AACGCTTCACGAATTTGCGT-3ʹ; Reverse-5ʹ- CTCGCTTCGGCAGCACA-3ʹ).

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10

Quantifying mRNA and miRNA Levels in CDDP-resistant OS

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Total RNA from CDDP-resistant OS tissues or cells was extracted using an RNA extraction kit (Solarbio). The random primers (Solarbio) were used to perform reverse transcription, and the qRT-PCR was carried out on Thermal Cycler CFX6 System (Bio-Rad, California, USA) with SYBR mix (TaKaRa, Dalian, China). The amplification parameters were: denaturation at 95°C for 10 min, followed by 40 cycles of denaturation at 95°C for 30s, annealing at 60°C for 30s and extension at 72°C for 1min. The levels of OIP5-AS1 and FOSL2 were normalized by glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and the level of miR-377-3p was standardized via small nuclear RNA U6, then calculated with the method of 2−ΔΔCt. The primer sequences were presented as follows: OIP5-AS1 (F, 5ʹ-TGCGAAGATGGCGGAGTAAG-3ʹ, R, 5ʹ-TAGTTCCTCTCCTCTGGCCG-3ʹ); miR-377-3p: (F, 5ʹ-GGGAGGCAGTGTATTGTTA-3ʹ, R, 5ʹ-CAGTGCGTGTCGTGGAGT-3ʹ); FOSL2 (F, 5ʹ-GAGAGGAACA AGCTGGCTGC-3ʹ, R, 5ʹ-GCTTCTCCTTCTCCTTCTGC-3ʹ); GAPDH (F, 5ʹ-TGTTCGTCATGGGTGTGAAC-3ʹ, R, 5ʹ-ATGGCATGGACTGTGGTCAT-3ʹ), and U6 (F, 5ʹ-ATTGGAACGATACAGAGAAGATT-3ʹ, and R, 5ʹ-GGAACGCTTCACGAATTTG-3ʹ).
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