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Quantstudio design analysis software v1

Manufactured by Thermo Fisher Scientific
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The QuantStudio Design & Analysis Software v1.5.1 is a comprehensive software solution developed by Thermo Fisher Scientific for the analysis and design of quantitative PCR (qPCR) experiments. The software provides a user-friendly interface for data visualization, analysis, and reporting.

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33 protocols using quantstudio design analysis software v1

1

Quantification of Apoptosis-related Genes

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Total RNA from all cell lines was isolated using High Pure RNA Isolation Kit from Roche following the manufacturer’s protocol. RNA was extracted from cellular pellet from around 1 × 106 total cells. RNA concentration was measured using a NanoDrop ND 2000-UV-vis Spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA). cDNA synthesis was performed using the High-Capacity cDNA Reverse Transcription kit (Applied Biosystems TM by Life Technologies TM, Carlsbad, CA, USA). We used TaqMan® Gene Expression Assays (Applied BiosystemsTM by Life TechnologiesTM, Carlsbad, CA, USA). Primers used in the assay were BAX and CASPASA-3 (proapoptotic genes); BCL-2 (antiapoptotic gene) and GAPDH as endogenous control, carried out by quantitative real time-PCR (qRT-PCR) in RNA extracted from cell lines. Normalization was performed with GAPDH. The data were managed using the QuantStudio™ Design & Analysis Software v1.4 (Applied Biosystems ™ by Life Technologies ™, Carlsbad, California, USA). Relative expression was calculated using the comparative Ct method and obtaining the fold-change value (ΔΔCt).
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2

Quantitative Analysis of Gene Expression

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Total RNA was extracted from hTERT-RPE cells treated with DMSO or BFA using RNeasyR mini kit (Qiagen). DMSO or BFA was treated 30 min before serum-restimulation at the indicated concentrations. cDNA was generated by SuperScript III Reverse Transcriptase (Invitrogen) according to the manufacturer’s instructions. Conventional RT-PCR was performed using a ProFlex™ Base Thermal Cycler (Applied Bio-systems) with the conditions of 95°C for 20 s, 62°C for 30 s, and 72°C for 45 s for a total of 25 cycles for Plk1, Dvl2, and GAPDH, followed by a 10 min final extension at 72°C. PCR products were electrophoresed in 3% agarose gel, stained with EcoDye™ Nucleic Acid Staining Solution (BIOFACT, Korea), and photographed. Real-time RT-PCR was performed in a final volume of 20 μl with 2 μl of cDNA, 10 pmol forward and 10 pmol reverse primer in 1X power SYBG green PCR master Mix (Applied Biosystems, USA) with the condition of 95°C for 15 s for denaturation, 55°C for 1 min for annealing and 72°C for 15 s extension using an QuantStudio™ 3 Real-Time PCR System (Applied Biosystems). The expression value of each gene was normalized by that of GAPDH. Final values were calculated using the ΔΔCt method. The results were analyzed using QuantStudio™ design & Analysis software v1.4 (Applied Biosystems). All the primers used in these experiments are summarized in Supplementary Table S3.
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3

SARS-CoV-2 Detection via One-Step RT-qPCR

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Five microlitre of total RNA was used for one-step cDNA synthesis and RT-qPCR reaction in a total volume of 20 µL consisting of 20× Primer-Probe Mix for SARS-CoV-2 Detection (#PPM, Diagnolita) [11 (link)], 4× TaqMan Fast Virus 1-Step Master Mix (Thermo Fisher Scientific (TFS), Waltham, MA, USA), and RNase-free water. For cDNA synthesis, reaction mixes were incubated at 50°C for 5 min, and the subsequent RT-qPCR runs consisted of enzyme activation at 95°C for 20 s and 40 cycles of 95°C for 3 s and 60°C for 30 s. RT-qPCR reactions were run on the QuantStudio 5 Real-Time PCR System by using QuantStudio Design & Analysis Software v1.4.1 (both from Applied Biosystems, TFS).
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4

Quantitative Gene Expression Analysis

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Total RNA was extracted with Quick-Zol (Kalium Technologies, Bernal, Argentina) and reverse transcribed using the RevertAid RT kit (Fermentas, Waltham, MA, USA). Quantitative real-time PCR (qPCR) was performed on a QuantStudio 3 thermocycler (Applied Biosystems, Waltham, MA, USA) using FastStart Universal SYBR Green Master (ROX) 1X (Roche, Rotkreuz, Switzerland). Primer sequences (5′-3′) used were: PPIA: GGTATAAAAGGGGCGGGAGG and CTGCAAACAGCTCAAAGGAGAC; PKM2: TGCAGTGGAGCTCAGAGAGA and GTCTGAATGAAGGCAGTCCC; ACO2: ACAGCCTACTGGTGACTCGG and GCTCAAAGTGGCTCATCGC; LDHA: TTGTTGGGGTTGGTGCTGTTG and TGGTGTTCTAAGGAAAAGGCTG; LDHB: GGTTGAAAGTGCCTATGAAGTC and TACATGGAAGGCTCAGGAAGA; SLC2A1: GTCTGGCATCAACGCTGTCT; AACAGCGACACGACAGTGAA. Each sample was run in triplicate and PPIA was used as a reference gene. Data were obtained with the QuantStudio Design & Analysis Software v1.4.1 (Applied Biosystems, Waltham, MA, USA) and analysis was based on the ΔΔCt method [38 (link)].
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5

MicroRNA Expression Analysis Protocol

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The miRNA expression analysis was performed in duplicate for the following miRNAs using miRCURY LNA miRNA PCR Assays (Qiagen): let-7b-5p, hsa-miR-140-3p, hsa-miR-9-5p, hsa-miR-16-5p, hsa-miR-21-5p, hsa-miR-25-5p, hsa-miR-34a-5p, hsa-miR-191-5p, hsa-miR-200a-3p, hsa-miR-203a-3p, hsa-miR-218-5p. U6 snRNA and SNORD48 were chosen for the normalization of miRNA expression. Real-time PCR was performed using the QuantStudio5 thermal cycler (Thermo Fisher Scientific). The reaction was performed using miRCURY LNA SYBR Green Master Mix (Qiagen) according to the manufacturer’s recommendations. The initial data analysis was prepared using QuantStudio Design & Analysis Software v1.5.1 (Thermo Fisher Scientific) to obtain raw Ct values. The relative quantification of miRNAs expression was determined.
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6

RNA Extraction and Real-Time PCR Analysis

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Total RNA was extracted from mouse tissues with Trizol. First-strand cDNA was synthesized using RevertAid RT Reverse Transcription Kit (K1691, Thermo Fisher Scientific, Waltham, MA). Real-time PCR was performed using PerfeCTa SYBR Green FastMix (95074, QuantaBio, Beverly, MA) in QuantStudioTM 5 Real-Time PCR Systems with QuantStudio Design & Analysis software v1.5.1 (Thermo Fisher Scientific). Samples were normalized for expression of Gapdh and analyzed by the 2−ΔΔCt method.
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7

Quantitative RT-PCR for FMR1 Gene

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qRT-PCR analysis and FMR1 quantification were done with the QuantStudio Design & Analysis Software v1.5.1 (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.) using the automatic baseline threshold algorithm combined with the standard curve method. The standard curve was plotted with cycle threshold (Ct) on the y-axis and the quantity of each standard point on the x-axis. Quantities of the samples were interpolated from their Ct values using the standard curve.
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8

FMDV Detection by Real-Time RT-PCR

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Viral RNA was extracted from 100 μL of cell culture supernatants using the ID Gene Mag Universal kit (Innovative Diagnostic) and a KingFisher Flex automat, according to the supplier’s recommendations in an elution volume of 60 μL. Molecular FMDV detection was performed by real-time (rt) RT-PCR targeting 3Dpol gene, as well as GAPDH housekeeping gene (Bernelin-Cottet et al., in prep.) using AgPath-ID One-Step RT-PCR kit in a final volume of 25 μL. For each PCR, 12.5 μL of buffer 2X, 1 μL of RT-PCR enzyme mix 25X according to suppliers’ recommendations, and each primer and TaqMan probe at 0.2 μM were mixed with 5 μL of sample RNA. PCR amplifications were performed with a QuantStudio™5 Real-Time PCR Instrument (Life Technologies) for 10 min at 45°C, for 10 min at 95°C followed by 45 cycles composed of 15 s at 95°C, and for 1 min at 60°C. Results were analyzed with the QuantStudio Design & Analysis software v1.5.1 (Thermo Fisher Scientific).
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9

Robust qPCR Reference Gene Validation

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Candidate reference gene primer/probe mixes were purchased from Integrated DNA Technologies as pre-validated probe PrimeTime® qPCR Probe Assays using TaqMan based chemistry (Table 1). Table 2 highlights the primer and probe sequences, location of the primers and the average efficiencies of the primers in previous experiments using 2-fold serial dilutions; primer efficiency was calculated as 10(− 1/slope). Quantitative PCR was performed using the QuantStudio™ 5 Real Time PCR System (Applied Biosystems); briefly, 2 μL of cDNA of each sample was loaded in duplicate into 96-well plates and 8 μL of qPCR master mix was added, which included TaqMan Fast Advanced Master Mix (5 μL; Applied Biosystems), reference gene primer/probe mix (0.5 μL), and RNase/DNase free H2O (2.5 μL; Qiagen)). Negative controls (no RNA or cDNA) were included to verify the absence of contamination. Amplification was performed at 60 °C using a two-step cycling procedure for 40 cycles, and resultant quantification cycles (Cq) were calculated using the default settings in the QuantStudio Design & Analysis Software v1.4.3 (Applied Biosystems).
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10

Quantifying Ovarian Cancer Biomarkers

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The RNA samples from ovarian cancer cell cultures and tissue samples were used for the quantitative analysis of NOTCH receptors (NOTCH1-4), FBXW7 and the β -catenin gene CTNNB1, as well as the chromatin-remodelling complex SWI/SNF subunit coding gene ARID1A mRNA transcripts. First, cDNA was synthesised from the total RNA samples using the Maxima First Strand cDNA Synthesis Kit for RT–qPCR with dsDNase (ThermoScientific, TFS, Vilnius, Lithuania) on a ProFlex PCR System (Applied Biosystems, TFS, Singapore). The resulting cDNA was used for quantitative PCR (qPCR) using a Maxima SYBR Green qPCR Master Mix (2X) kit (ThermoScientific, TFS, Vilnius, Lithuania) on a QuantStudio 5 Real-Time PCR System (Applied Biosystems, TFS, Singapore). The primer sequences are provided in Appendix A Table A1. All qPCR reactions were performed in duplicate according to the manufacturer’s protocol. The initial Ct values were gathered using QuantStudio Design & Analysis Software v1.4.3 (Applied Biosystems) with automatic baseline. Then, the data were normalized to a reference gene (GAPDH) and log2 2ΔCt values and used for further statistical analysis.
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