Quantstudio 5 platform

Manufactured by Thermo Fisher Scientific

Sourced in United States, Switzerland

The QuantStudio 5 platform is a real-time PCR system designed for gene expression, genotyping, copy number variation, and other nucleic acid analysis applications. The platform features a 96-well format and supports multiple sample types, including DNA, RNA, and cDNA. The system utilizes advanced optics and thermal cycling technology to provide accurate and reliable results.

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Lab products found in correlation

Cobas 6800 platform, by Roche (2 mentions) Mammalian total rna miniprep kit, by Merck Group (1 mentions) Quantifast sybr green pcr kit, by Qiagen (1 mentions) Iscript cdna synthesis kit, by Bio-Rad (1 mentions) Ribonuclease inhibitor, by Thermo Fisher Scientific (1 mentions) Dntp mix, by Thermo Fisher Scientific (1 mentions) M mlv reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Dithiothreitol (dtt), by Thermo Fisher Scientific (1 mentions)

7 protocols using quantstudio 5 platform

Post-Infection Symptom Monitoring Protocol

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At the follow-up blood collections (five months and ten months post-infection), participants were asked to complete a written questionnaire, providing information about vaccination and infection status, and the duration of persistent symptoms (Long-COVID symptoms).
If participants had any symptoms during the study period, they were encouraged to visit the Liechtenstein National Testing Facility for reverse transcription-polymerase chain reaction (RT-PCR) testing, which was performed with either the COBAS 6800 platform (Roche Diagnostics, Rotkreuz, Switzerland) or the TaqPath assay on a QuantStudio 5 platform (Thermo Fisher Scientific, Allschwil, Switzerland) [24 (link),25 (link),26 (link)]. Positively tested participants (PCR and antibody tests, or only antibody tests) were subsequently contacted by the study team and asked to report their symptoms (fever, fever degree, chills, cough, sniff, dyspnea, anosmia, ageusia, pressure in the chest, sore throat, muscle pain, headache, fatigue, general feeling of illness, diarrhea, sickness, vomiting) and hospitalization status by a standardized questionnaire commissioned by telephone interview (Figure 2).

Telser J., Grossmann K., Weideli O.C., Hillmann D., Aeschbacher S., Wohlwend N., Velez L., Kuhle J., Maleska A., Benkert P., Risch C., Conen D., Risch M, & Risch L. (2023). Concentrations of Serum Brain Injury Biomarkers Following SARS-CoV-2 Infection in Individuals with and without Long-COVID—Results from the Prospective Population-Based COVI-GAPP Study. Diagnostics, 13(13), 2167.

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Quantitative Real-Time PCR Analysis

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Total RNA was isolated from colonic tissues using the Mammalian Total RNA Miniprep Kit (Cat# AG11706, Sigma-Aldrich, St. Louis, MO, USA). Reverse transcription of RNA to cDNA was performed with the Evo M-MLV RT Master Mix (Agbio, Hunan, China) according to the manufacturer’s instructions. Quantitative real-time PCR (qRT-PCR) was then conducted using the SYBR Green Premix Pro Taq HS qPCR Kit (Cat# AG11718, Agbio) on a QuantStudio5 platform (Thermo Fisher Scientific, Waltham, MA, USA). Primer sequences used for qRT-PCR are listed in Supplementary Table S1. Gene expression levels were normalized to Gapdh.

Qiu D., Xu S., Ji K, & Tang C. (2024). Myeloid Cell-Derived IL-1 Signaling Damps Neuregulin-1 from Fibroblasts to Suppress Colitis-Induced Early Repair of the Intestinal Epithelium. International Journal of Molecular Sciences, 25(8), 4469.

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Quantifying Flavonoid Synthesis Genes

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Twelve selected DEGs involved in flavonoid synthesis were determined by RT-qPCR. Total RNA was extracted from the 24 samples (in triplicate) as described above. First-strand cDNA was synthesized from 0.1 μg of total RNA by the manufacturer’s instruction (Vazyme, R223–01). The reactions were performed using a QuantiFast® SYBR® Green PCR Kit (Qiagen, Germany), and RT-qPCR was carried out on an Applied Biosystems QuantStudio™ 5 platform (Thermo Fisher Scientific, Waltham, MA, USA). The primers were designed with the Primer premier 5.0 software and synthesized by TsingKe Biological Technology Co., Ltd. (Xi’an, China) (Table S1). Rer1 (JZ818481) was used as an internal standard [39 (link)]. The relative expression levels of genes were calculated using the 2^−ΔΔCt method [40 (link)].

Duan H.R., Wang L.R., Cui G.X., Zhou X.H., Duan X.R, & Yang H.S. (2020). Identification of the regulatory networks and hub genes controlling alfalfa floral pigmentation variation using RNA-sequencing analysis. BMC Plant Biology, 20, 110.

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Seroconversion and COVID-19 Symptom Duration

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SARS-CoV-2 antibody tests were assessed at baseline (starting April 2020) and during follow-up (starting December 2020) by the medical laboratory Dr. Risch Ostschweiz AG (Buchs SG, Switzerland). The tests were assessed with an orthogonal test algorithm that employed electrochemiluminescence assays. These assay test for pan-immunoglobulins directed against the N antigen and the receptor-binding domain of the SARS-CoV-2 spike protein.19 (link) Seroconversion was assumed if the first blood sample was negative for SARS-CoV-2 antibodies and the second sample was positive.
If participants had any symptoms during the study period, they were encouraged to visit the Liechtenstein National Testing Facility for RT-PCR testing. The testing facility was open daily allowing for higher testing frequencies than that in other European countries.20 (link) RT-PCR was performed on either the COBAS 6800 platform (Roche Diagnostics, Rotkreuz, Switzerland) or the TaqPath assay on a QuantStudio 5 platform (Thermo Fisher Scientific, Allschwil, Switzerland).20–22 (link) Participants diagnosed with COVID-19 contacted the study team to discuss their symptoms and health statuses. Additionally, participants provided their date of SO and overall symptom duration, enabling us to calculate the symptom end (SE) date.

Risch M., Grossmann K., Aeschbacher S., Weideli O.C., Kovac M., Pereira F., Wohlwend N., Risch C., Hillmann D., Lung T., Renz H., Twerenbold R., Rothenbühler M., Leibovitz D., Kovacevic V., Markovic A., Klaver P., Brakenhoff T.B., Franks B., Mitratza M., Downward G.S., Dowling A., Montes S., Grobbee D.E., Cronin M., Conen D., Goodale B.M, & Risch L. (2022). Investigation of the use of a sensor bracelet for the presymptomatic detection of changes in physiological parameters related to COVID-19: an interim analysis of a prospective cohort study (COVI-GAPP). BMJ Open, 12(6), e058274.

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Isolation and qPCR of Neuronal Markers

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RNA was isolated using Trizol and phenol/chlorofom extraction. cDNA synthesis was performed using 1 μg of RNA and an iScript cDNA synthesis kit (BioRad). qPCR was performed using Taqman assays and reagents against ActB, GFAP, and MAP2 on a QuantStudio 5 platform (ThermoFisher).

Flannagan K., Stopperan J.A., Hauger B.M., Troutwine B.R., Lysaker C.R., Strope T.A., Csikos Drummond V., Gilmore C.A., Swerdlow N.A., Draper J.M., Gouvion C.M., Vivian J.L., Haeri M., Swerdlow R.H, & Wilkins H.M. (2023). Cell type and sex specific mitochondrial phenotypes in iPSC derived models of Alzheimer’s disease. Frontiers in Molecular Neuroscience, 16, 1201015.

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Quantitative PCR of Heart Tissue

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Total RNA from the heart tissues was purified using an RNA purification kit (cat. no. 12183025; Invitrogen; Thermo Fisher Scientific, Inc.). The first-strand cDNA was synthesized using oligo(dT)_12-18 primers (cat. no. 18418012; Invitrogen; Thermo Fisher Scientific, Inc.), dNTP Mix (cat. no. 18427-013; Invitrogen), Ribonuclease Inhibitor (cat. no. 10777-019; Invitrogen), DTT (cat. no. Y00147; Invitrogen), and M-MLV Reverse Transcriptase (cat. no. 28025-013; Invitrogen). The reaction process was under 37°C for 50 min and then was terminated at 70°C for 15 min. qPCR was performed using SYBR green PCR master mix (cat. no. 4367659; Applied Biosystems; Thermo Fisher Scientific, Inc.) using the Applied Biosystems QuantStudio 5 platform and the amplification conditions (95°C for 5 min followed by 45 cycles of 95°C for 15 s, 55°C for 15 s and 72°C for 20 s) were set as previously described (16 (link)). Gene specific primers (Table I) were provided by Sangon Biotech Co., Ltd. The relative RNA expression levels were calculated using 2^−ΔΔCq (21 (link)) and normalized against the housekeeping gene, 18S rRNA.

Weng W., Yu X., Dong Y., Wang T., Shao M., Sun H, & Han P. (2023). Artemether ameliorates adriamycin induced cardiac atrophy in mice. Molecular Medicine Reports, 28(2), 153.

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Quantitative Real-Time PCR Protocol

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Quantitative Real-Time Polymerase Chain Reaction (qPCR) was performed using the Accuris qMAX One-Step RT-qPCR kits (Accuris Instruments, Edison, NJ, USA) on the Applied Biosystems’ Quant Studio 5 platform (PE Applied Biosystems, Waltham, MA, USA). The experiments used a 25 µL reaction volume and thermo profile as shown in Table 2. The relative gene expression was calculated using the delta-delta thresh-hold cycle (ΔΔCt) formula ΔCt = Ct (gene of interest)—Ct (housekeeping gene) according to [20 (link)]. All primer sets used in the study are listed in Table 3.

Mudenda M., Kimani J., Kinyua J, & Kimotho J. (2022). Preliminary In Vivo Evidence of Oral Selenium Supplementation as a Potentiating Agent on a Vector-Based COVID-19 Vaccine in BALB/c Mice. Vaccines, 11(1), 57.

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