Reference material DNA samples were identified from the 1000 Genomes Project v3 dataset using VarCover (https://varcover.org/ ) (E. R. Scott, Bansal, Meacham, & Scott, 2020 (link)) and acquired from the Coriell Institute for Medical Research (Camden, NJ) (Table 1 ). Additional de-identified NUDT15 DNA controls with blinded results from previous testing were provided by St. Jude Children’s Research Hospital. In addition, peripheral blood DNA samples were obtained from 100 unrelated, healthy Ashkenazi Jewish individuals from the greater New York City metropolitan area as previously described (S. A. Scott, Edelmann, Kornreich, & Desnick, 2008 (link); S. A. Scott et al., 2010 (link); S. A. Scott et al., 2012 (link)). All personal identifiers were removed and isolated DNA samples were tested anonymously. Peripheral blood was collected in EDTA vacutainer tubes using standard practices and DNA was isolated using the QiaSymphony (Qiagen, Valencia, CA) or Chemagic (Perkin Elmer, Baesweiler, Germany) according to manufacturer instructions. Saliva samples were collected using the Oragene Dx kit (OGD-500; DNA Genotek, Ottawa, ON, Canada) and DNA was isolated using the QiaSymphony (Qiagen).
Qiasymphony
Manufactured by Qiagen
Sourced in Germany, United States, Netherlands, Canada, France, Spain
The QIAsymphony is an automated sample processing platform designed for high-throughput nucleic acid isolation and purification. It provides a fully integrated and standardized workflow for processing a wide range of sample types, enabling efficient and reliable sample preparation for downstream applications.
Automatically generated - may contain errors
Lab products found in correlation
Nanodrop, by Thermo Fisher Scientific (10 mentions)
Qubit fluorometer, by Thermo Fisher Scientific (10 mentions)
Hiseq 2500, by Illumina (9 mentions)
Dsp dna mini kit, by Qiagen (7 mentions)
Qiasymphony dsp virus pathogen kit, by Qiagen (6 mentions)
Multiskan go, by Thermo Fisher Scientific (6 mentions)
Dsp virus pathogen midi kit, by Qiagen (5 mentions)
Dsp virus pathogen mini kit, by Qiagen (4 mentions)
Qiasymphony dsp virus pathogen midi kit, by Qiagen (4 mentions)
Novaseq 6000, by Illumina (4 mentions)
Lightcycler 480, by Roche (4 mentions)
Qiaamp dna blood mini kit, by Qiagen (3 mentions)
Tissuelyser lt, by Qiagen (3 mentions)
Bigdye terminator v1.1 cycle sequencing kit, by Thermo Fisher Scientific (3 mentions)
Perfecta qpcr toughmix, by Quanta Biosciences (3 mentions)
Taqpath pcr covid 19 combo kit, by Thermo Fisher Scientific (3 mentions)
Abi 7500 thermal cycler, by Thermo Fisher Scientific (3 mentions)
Xpert xpress sars cov 2, by Cepheid (3 mentions)
Miseq platform, by Illumina (3 mentions)
Rotor gene q, by Qiagen (3 mentions)
189 protocols using qiasymphony
1
Genetic Diversity Analysis of Ashkenazi Jews
2
Diverse DNA Sample Collection and Extraction
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Reference material DNA samples were identified and acquired from the Coriell Institute for Medical Research (Camden, NJ). Additional de‐identified DNA controls were isolated from peripheral blood that had previously undergone clinical genetic testing at Sema4 (formerly the Mount Sinai Genetic Testing Laboratory). Peripheral blood was collected in EDTA vacutainer tubes using standard practices and DNA was isolated using the QiaSymphony (Qiagen, Valencia, CA) or Chemagic (Perkin Elmer, Baesweiler, Germany) according to the manufacturer’s instructions. Saliva samples were collected using the Oragene Dx kit (OGD‐500; DNA Genotek, Ottawa, ON, Canada) and DNA was isolated using the QiaSymphony (Qiagen, Valencia, CA). Buccal samples were collected using the ORAcollect kit (OC‐175) and DNA was isolated using the prepIT•L2P protocol (DNA Genotek, Ottawa, ON, Canada), as per the manufacturer instructions.
3
Comparative Plasma DNA Extraction Kits
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For comparison of blood stabilisation and plasma volume the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) was used. In addition, a comparison of three DNA extraction kits was performed on equal volumes of plasma (2 mL each) (Fig 1B ). The following kits were used: PME free-circulating DNA Extraction Kit protocol (Analytik Jena, Jena, Germany) for 2–5 mL extractions using lysis solution GS/Binding solution VL system and DSP Virus/Pathogen Midi Kit performed on QIAsymphony (Qiagen) and the QIAamp Circulating Nucleic Acid Kit (QIAGEN). QIAsymphony extractions were performed at the Qiagen applications lab (Hilden). All plasma samples were processed according to the manufacturers’ protocols with the exception of the PME kit where an initial 20 min incubation instead of 10 min was performed and the plasma centrifugation steps were carried out at 3750 x g vs 4500 x g. All DNA was eluted in 80 μL within the range specified by the kit.
4
Nile Tilapia Fin Clip Sampling and DNA Extraction
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A total of 160 Nile tilapia fin clip samples derived from eight strains (n = 20 per strain) were collected from seven different hatcheries located in different regions in Tanzania: Silver-YY, BIG NIN, Chitralada-N, Chitralada-E, GIFT, Ruvu Farm-R, Chifive-C and Muleba-M (Table 1; Fig. 1). Regarding the GIFT strain, no information was available, whether it directly originated from the World Fish Center. Fish were reared in labelled plastic tanks of 1.5 m × 1.5 m × 1.5 m at the Institute of Marine Sciences Mariculture Centre (IMS-MC) at Bweni village, Pangani District in Tanga, Tanzania. Fin clips approximately 1.5-cm long were taken and preserved in 95% ethanol and stored at -20 °C. Total genomic DNA was extracted with the QIAsymphony kit using an automated DNA extraction robot (QIAsymphony, QIAGEN, Germany) according to the manufacturer's instructions. Following the DNA extraction, quantification of DNA samples was done using Qubit fluorometer (Thermo Fisher Scientific, USA ) and diluted by TE buffer to 20 ng/μL followed by gel electrophoresis (1% agarose gel) to assess DNA quality.
5
SARS-CoV-2 Assay Analytical Performance
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Limit of detection (LOD) of the SORP triplex assay was determined using AmpliRun™ Total SARS-CoV-2 control (Vircell, Granada, Spain), an inactivated (swab) SARS-CoV-2 viral control preparation (4.3 × 104 copies/mL). Post-reconstitution in sterile water as per the manufacturer's instructions, the SARS-CoV-2 inactivated virus control was extracted on the QIAsymphony (Qiagen) automated extraction platform, using the DSP Virus/Pathogen kit (Qiagen). Probit regression analysis to determine the 95% detection limit was carried out using the MedCalc Software package (MedCalc Software Ltd, Ostend, Belgium).
The analytical specificity of the SORP assay was evaluated using two methods: in silico analysis using BLAST analysis with common non-target organisms in the NCBI GenBank database (Table. 1 _Suppl) and RT-qPCR analysis on a panel of non-target microorganisms. These non-target microorganisms were either positive patient specimens (nasopharyngeal/oropharyngeal swabs, bronchoalveolar lavage fluid, urine, saliva, and nasal washes), type strain cultures or commercial standards (Table. 2 _Suppl). Nucleic acid was extracted from each individual organism using the QIAsymphony (Qiagen, Hilden, Germany) automated extraction platform.
The analytical specificity of the SORP assay was evaluated using two methods: in silico analysis using BLAST analysis with common non-target organisms in the NCBI GenBank database (
6
HDV RNA Quantification in Chronic Patients
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Serum and plasma samples were collected from chronic HDV RNA-positive patients who visited the outpatient clinic at INMI L Spallanzani IRCCS Medical Center/Hospital, Rome (Italy), for routine clinical and virological assessment. Total RNA was extracted from 400 µL of each sample using the automated system QIASYMPHONY (QIAGEN, Hilden, Germany). HDV RNA was quantified by Real-Time PCR using the Bosphore Quantitation-Detection Kit v1 (Anatolia Geneworks, Sultanbeyli, Turkey) with a limit of detection of 100 copies/mL and the 7500 TaqMan platform with a dynamic range of 103 to 108 copies/mL.
7
Automated Genomic DNA Extraction from Whole Blood
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Genomic DNA extraction from whole blood was performed using the QIAsymphony automated workstation, following the instructions of the manufacturer (Qiagen, United States).
8
SARS-CoV-2 Detection by Real-time RT-PCR
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Microbiological diagnosis of SARS-CoV-2 infection was performed by detection of SARS-CoV-2 RNA in respiratory samples (oropharyngeal-nasopharyngeal swab, bronchoalveolar lavage or broncoaspirate), as previously described (Bartoletti et al., 2020 (link)). Briefly, total DNA/RNA was extracted from samples by QiaSymphony (QIAGEN) and detection of SARS-CoV-2 was performed by real-time RT-PCR targeting regions in the N gene following the US CDC protocol.
9
RhD Negative Maternal Blood Processing
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Samples from pregnant RhD‐negative women analysed from May 2019 to October 2020 were included.
Whole blood samples, 5 or 7 ml EDTA tubes, were collected at antenatal or blood sampling centres and sent to the laboratory by regular post or transportation service. Only blood samples no older than 5 days were accepted for analysis. The samples were centrifuged for 15 min at 1500g. The blood tubes, were in most cases, put directly onto the QIAsymphony (QIAGEN, Hilden, Germany) instrument for DNA extraction but for samples close to 5 days before they could be analysed, plasma was transferred to cryotubes and frozen at −20°C until further analysis. As shown by others, the use of short‐time frozen plasma does not have a major effect on results [13 (link)].
Whole blood samples, 5 or 7 ml EDTA tubes, were collected at antenatal or blood sampling centres and sent to the laboratory by regular post or transportation service. Only blood samples no older than 5 days were accepted for analysis. The samples were centrifuged for 15 min at 1500g. The blood tubes, were in most cases, put directly onto the QIAsymphony (QIAGEN, Hilden, Germany) instrument for DNA extraction but for samples close to 5 days before they could be analysed, plasma was transferred to cryotubes and frozen at −20°C until further analysis. As shown by others, the use of short‐time frozen plasma does not have a major effect on results [13 (link)].
10
Placental and Umbilical Cord Biosampling
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