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Stepone plus system software

Manufactured by Thermo Fisher Scientific
Sourced in United States

The StepOne Plus™ system software is a core component of the StepOne Plus™ real-time PCR system. It provides the necessary functionality to operate and control the hardware, as well as analyze the data generated from real-time PCR experiments.

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6 protocols using stepone plus system software

1

Quantitative Gene Expression Analysis Using RT-PCR

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Total RNA from cell pellets was isolated using TRIzol reagent and quantified using a spectrophotometer. The cDNA was synthesized in a total reaction volume of 20 μl; the reaction mixture contained 2 μg of total RNA, oligo (dT), and reverse transcription premix under the following reaction conditions: 45°C for 45 min, followed by 95°C for 5 min. Gene expression was quantified using RT-PCR, and the resultant data were analyzed using the StepOne Plus™ system software (Applied Biosystems, Foster City, CA, United States). RT-PCR amplifications were performed using SYBR Green PCR Master Mix with premixed ROX (Applied Biosystems, Foster City, CA, United States) and primers (Bioneer, Daejeon, Korea) in an ABI 7300 instrument according to the manufacturer’s protocol. The reaction conditions were as follows: initiation at 95°C for 10 min, followed by cycling conditions of 95°C for 15 s, 60°C for 30 s, and 72°C for 30 s for 40 cycles. Beta-actin was used as an internal control.
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2

Genotyping of CHRNA6 Gene Variants

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Genomic DNA was extracted from each blood sample using QIAamp DNA Bloodkit (Qiagen, CA). Three tagging SNPs were identified within CHRNA6 gene locus using the Haploview Tagger program: rs892413 (MAF=0.21); rs1072003 (MAF= 0.18), and rs7828365 (MAF=0.12). Tagging SNPs were genotyped using the 5’ nuclease method (76 (link)) and predesigned ABI SNP assays. Allele-specific signals were distinguished by measuring endpoint 6-FAM or VIC fluorescence intensities at 508 nm and 560 nm, respectively; genotypes were generated using StepOnePlus System Software (Applied Biosystems). The genotyping error rate was directly determined by re-genotyping 25% of the samples, randomly chosen, for each locus. Data cleaning and analysis were implemented using PLINK software v1.07 (77 (link)). Standard genotyping quality filters were imposed (call rate >95%, Hardy-Weinberg equilibrium P>5×10−5).
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3

Quantification of Immune Gene Expression

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PAXgene whole blood mRNA expression of HSD11β-1, IL-1β, IFN-γ, and TNF-α were assessed by quantitative polymerase chain reaction (qPCR). Collection of 2.5 mL of blood was taken into PAXgene mRNA tubes from each participant at the time of recruitment and were stored as per manufacturer’s instructions. Total RNA was isolated from the whole blood and equalized before it was used for cDNA synthesis. Analysis of gene expression of the target gene was conducted using Real-Time PCR methods and Taqman® Gene Expression Assays (Applied Biosystems, Foster City, CA, USA). At the end of the reaction, data analysis was performed with the StepOnePlus™ System Software (Applied Biosystems, Foster City, CA, USA) and ExpressionSuite Software (Applied Biosystems, Foster City, CA, USA) for inter-plate normalization. Relative Quantification (RQ) values (2−ΔΔCt, where Ct is the threshold cycle) of the target genes relative to their own endogenous control were obtained.
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4

Quantitative RT-PCR Analysis of Gene Expression

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Total RNA was isolated from cell pellets using Trizol reagent and quantified by spectrophotometry. The cDNA was synthesized in a 20 µL reaction containing 2 µg of total RNA, oligo (dT), and Reverse Transcription Premix under the following reaction conditions: 45 °C for 45 min and 95 °C for 5 min. Gene expression signals were quantified using real-time RT-PCR. The data were analyzed using the StepOne PlusTM system software (Applied Biosystems, Foster City, CA, USA). RT-qPCR amplifications were performed using SYBR Green PCR Master Mix with premixed ROX (Applied Biosystems, Foster City, CA, USA) and primers (Bioneer, Daejeon, Korea) in an ABI 7300 following the manufacturer’s protocol. Reaction conditions were as follows: initiation at 95 °C for 10 min, followed by cycling conditions of 95 °C for 15 sec, 55 °C for 30 sec, and 72 °C for 30 sec for 40 cycles. The expression of β-actin was used as an internal control.
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5

Quantifying Gene Expression by RT-PCR

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To isolate and quantify the total RNA from the cell pellets, Trizol reagent was used, and the analysis was done using a spectrophotometer. The synthesis of cDNA was carried out in a total reaction volume of 20 µL; the reaction mixture consisted of 2 µg of total RNA, oligo (dT), and reverse transcription premix under the following reaction conditions: 45 °C for 45 min, followed by 95 °C for 5 min. RT-PCR was used for quantification of gene expression, and the results were subsequently analyzed using the StepOne PlusTM system software (Applied Biosystems, Foster City, CA, USA). RT-PCR amplifications were conducted using SYBR Green PCR Master Mix with premixed ROX (Applied Biosystems, Foster City, CA, USA) and primers (Bioneer, Daejeon, Korea) in an ABI 7300 instrument following the manufacturer’s protocol. The reaction conditions were as follows: initiation at 95 °C for 10 min, followed by cycling conditions of 95 °C for 15 s, 60 °C for 30 s, and 72 °C for 30 s for 40 cycles. β-actin was used as an internal control.
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6

Quantitative RT-PCR Analysis of Adipogenesis Markers

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Total RNA was isolated using TRIzol reagent (TaKaRa; Shiga, Japan), and approximately 2 µg of total RNA was synthesized to cDNA using Reverse Transcription Premix (Elpis-biotech; Daejeon, Korea Gene expression signals were quantified, and the data were analyzed using the StepOne PlusTM system software (v2.3, Applied Biosystems; Foster City, CA, USA). RT-qPCR amplification reactions were performed in a SYBR Green PCR Master Mix with premixed ROX (Applied Biosystems; Foster City, CA, USA). The following primer pairs (Bioneer, Daejeon, Korea) were used in the reactions performed in an ABI 7300 following the manufacturer’s protocol: β-actin (F: 5′-GGCCATCTCTTGCTCGAAGT-3′ and R: 5′-GACACCTTCAACACCCCAGC-3′), adiponectin (F: 5′-AAGGACAAGGCCGTTCTCT-3′ and R: 5′-TATGGGTAGTTGCAGTCAGTTGG -3′), PPARγ (F: 5′-AAACTCTGGGAGATTCTCCT-3′ and R: 5′-TGGCATCTCTGTGTCAAC-3′), SREBP-1a (F: 5′-GCTGCTGACCGACATCGAA-3′ and R: 5′-TCAAATAGGCCAGGGAAGTCA-3′), C/EBPα (F: 5′-GCCAAACTGAGACTCTTC-3′ and R: 5′-TGGCATCTCTGTGTCAAC-3′), and MMP-1 (F: 5′-CGAATTTGCCGACAGAGATGA-3′ and R: 5′-GAATTTGCCGACAGAGATGA-3′). The mRNA expression of β-actin was used as an internal control.
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