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Qiasymphony sp as instrument

Manufactured by Qiagen
Sourced in Germany

The QIAsymphony SP/AS instruments are automated sample preparation and assay setup systems designed for use in clinical and molecular diagnostic laboratories. The core function of these instruments is to automate the extraction and purification of nucleic acids (DNA and RNA) from a variety of sample types, as well as the setup of downstream assays. The instruments are capable of handling a wide range of sample volumes and types, and can be used with a variety of QIAGEN kits and reagents.

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12 protocols using qiasymphony sp as instrument

1

Exon Sequencing of TP53, KRAS, and BRAF in CRC

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Exon sequencing was performed to screen for mutations in the TP53, KRAS and BRAF genes in CRC patients’ tumors and metastasis. Sequencing was performed by W. Weichert and R. Penzel at the Institute for Pathology of the University of Heidelberg. Briefly, slices from formalin-fixed and paraffin-embedded tissues were deparaffinized via xylol-ethanol-treatment. Tumor tissue-rich segments of the slices were selected to purify genomic DNA (QIAsymphony DNA Mini Kit, QIAGEN, 937236). Samples were sequenced in a fully-atomized fashion employing QIAsymphony SP/AS instruments (QIAGEN, 9001297/9001301).
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2

Multiplex PCR for PVL and MRSA Detection

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DNA was extracted using the automated QIAsymphony SP/AS instruments (QIAGEN, Germany). A multiplex PCR was used targeting the genes encoding PVL (lukS-PV and lukF-PV) and mecA and mecC, as described previously [13 (link)].
Sequence-based typing of the hypervariable region of S. aureus protein A (spa-typing) was performed as described by Harmsen and colleagues [15 (link)]. Spa types were assigned using the Ridom StaphType software version 2.2.1 (Ridom GmbH, Würzburg, Germany). Cluster analysis of spa typing data was performed by application of the integrated Based Upon Repeat Patterns (BURP) algorithm as described elsewhere [16 (link)]. The associated MLST-based sequence types or MLST-CCs were allocated by the Ridom SpaServer (http://spaserver.ridom.de), retrieved from the literature [1 (link), 3 (link), 12 (link), 17 (link), 18 (link)], or derived from closely related spa-types.
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3

SARS-CoV-2 RNA Detection via RT-PCR

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To check for the presence of SARS-CoV-2 RNA, each filter underwent molecular investigation using the Polymerase Chain Reaction (PCR) method.
The viral target sequences were detected using real-time RT-PCR (target: N gene), using the reference method recommended by the Centers for Disease Control and Prevention [42 ], after extracting the nucleic acid with the help of semi-automatic equipment (QIAsymphony SP/AS instruments, manufactured by QIAGEN, Switzerland). The detection limit of this molecular method is 10−0.5 copies RNA/μl. Every amplification test included a positive control (K+), a negative control (K-) and an extraction process control to prove that the nucleic acid had been extracted correctly and the extraction reagent was working.
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4

Genotyping FOXO3 rs2802292 Polymorphism

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Genomic DNA from cell lines and primary fibroblasts was extracted using QIAsymphony SP/AS instruments (QIAGEN) according to the manufacturer’s protocol and quantified on a NanoDROP 2000 spectrophotometer (Thermo Scientific). Polymerase chain reactions (PCRs) were carried out in 25 μl reaction mixtures containing 50 ng of genomic DNA, 1× PCR buffer (Tris–HCl, (NH4)2SO4, 15 mM MgCl2; pH 8.7), 200 μM dNTPs (Thermo Fisher Scientific, R0181) and 0.5 U Taq DNA Polimerase Recombinant (Thermo Fisher Scientific, EP0405) and the following primers (10 pmol each): FOXO3 rs2802292g/t Fw and FOXO3 rs2802292g/t Rv. PCR amplification cycles were carried out at 95°C for 15 min followed by 29 cycles of denaturation at 94°C for 1 min, annealing at 60°C for 1 min and extension at 72°C for 1 min, and by a final extension at 72°C for 10 min on a GeneAmp PCR System 9700 thermocycler (Applied Biosystems). A total of 5 μl of the amplified products were loaded onto 2% Agarose Standard Low EEO (Sigma, A9539) in 0.5× Tris-Borate-EDTA (TBE) (Serva, 39320.01) and visualized using GelRed™ (Biotium, 41003). Sequencing products were purified by use of the DyeEx™ 2.0 Spin Kit (QIAGEN, 63206) and sequenced on an ABI PRISM 310 Genetic Analyzer (Applied Biosystems). Primer sequences are listed in ‘Additional Material’.
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5

Genomic DNA Extraction and FOXO3A Genotyping

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Genomic DNA from peripheral blood and cell lines was extracted using QIAsymphony SP/AS instruments (QIAGEN) according to the manufacturer’s protocol and quantified on a NanoDROP 2000 spectrophotometer (Thermo Scientific). PCRs were carried out in 25 μl reaction mixtures containing 50 ng of genomic DNA, 1X PCR Buffer (Tris–HCl, (NH4)2SO4, 15 mM MgCl2; pH 8.7), 200 μM dNTPs and 0.5 U HotStarTaq DNA Polimerase (QIAGEN) and the following primers (10 pmol each): FoxO3A rs2802292g/t Fw, cagcttctgagtgacagagtg and FoxO3A rs2802292g/t Rw, ttcttccctagagagcagcag. PCR amplification cycles were carried out at 95°C for 15 min followed by 29 cycles of denaturation at 94°C for 1 min, annealing at 60°C for 1 min and extension at 72°C for 1 min, and then a final extension at 72°C for 10 min on a GeneAmp PCR System 9700 thermocycler (Applied Biosystems). 5 μl of the amplified products were loaded onto 2% Agarose Standard Low EEO (AB Analitica) in 0.5X TBE and visualized using GelRedTM (Biotium, Hayward, CA). Sequencing products were purified by use of the DyeEx™ 2.0 Spin Kit (QIAGEN, Milan, Italy) and sequenced on an ABI PRISM 310 Genetic Analyzer (Applied Biosystems).
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6

HIV-1 Viral Load and CD4+ Count

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Plasma obtained from blood samples in EDTA was frozen at −80°C until tested.
The viral load in plasma was quantified using the Artus HI Virus-1 QS-RGQ Kit. The kit is a ready-to-use system for the detection of HIV-1 RNA using PCR on Rotor-Gene Q Instruments. Sample preparation and assay setup make use of the QIAsymphony SP/AS instruments (Qiagen), according to the manufacturer's instructions.
Lymphocyte surface phenotypes and CD4+ lymphocyte counts were determined using flow cytometry analysis by Immunotech-Beckman Coulter (Marseille, France).
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7

Automated Faecal DNA Extraction

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Microbial DNA will be extracted from 200 mg of faecal samples using the QIAsymphony® DSP Virus/Pathogen Mini-Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions on the QIAsymphony® SP (Qiagen). Automated isolation and pipetting of 96-well plates (MicroAmp Optical 96-Well Reaction Plate, Applied Biosystems, Darmstadt, Germany) will be performed by the QIAsymphony® SP/AS instrument (Qiagen) using the QIAsymphony DSP Virus/Pathogen Mini-Kit.
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8

Genomic DNA Extraction from Blood

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Genomic DNA was extracted from peripheral blood samples collected into 10 ml EDTA K2 blood collection tubes using the QIAsymphony® SP/AS instrument (Qiagen, Hilden, Germany) according to the manufacturer’s instruction. DNA quantity was estimated using the Qubit™ dsDNA HS Assay Kit on a Qubit 4.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA).
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9

CMV Reactivation Monitoring in Transplant

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CMV reactivation was defined as the presence of viral DNA above the detection threshold within the first four months post-transplant. Viral DNA was extracted from whole blood by using the QIAsymphony SP/AS instrument (Qiagen) and CMV DNA was detected and quantitated with a commercial real-time PCR assay (CMV ELITe MGB® kit, ELITech Group, Trezzano s/n, Milan, Italy). Sensitivity of the assay is 800 viral genomes per ml of whole blood.
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10

Microbial TNA Extraction from NP Swabs

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Total nucleic acid (TNA) extraction for microbial identification was conducted on NP swabs stored in Primestore ® MTM. Briefly, the samples were thawed and vortexed for 10 s, and 400 µl aliquots were transferred into ZR BashingBead ™ Lysis Tubes containing 0.5 mm beads (catalog no. ZR S6002-50, Zymo Research Corp., Irvine, CA, United States) for the mechanical lysis steps. Lysis was conducted on a Qiagen Tissue lyser LTTM (Qiagen, FRITSCH GmbH, Idar-Oberstein, Germany) for 5 min at 50 Hz, followed by centrifugation (Eppendorf F-45-30-11, Merck KgaA, Darmstadt, Germany) for 1 min at 10,000 rpm (10,640 g). The supernatants (250 µl) were extracted using the QIAsymphony ® DSP Virus/Pathogen Kit (Qiagen GmbH, Hilden, Germany) on the QIAsymphony SP/AS instrument (Qiagen GmbH, Hilden, Germany) following the manufacturer's instructions. The total nucleic acid was eluted in 70 µl DNA elution buffer into the Elution Microtube (Qiagen GmbH, Hilden, Germany) and immediately stored at -80 °C until further analysis.
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