At UFHealth Shands Hospital, 200 μl of patient sample in viral transport medium was extracted with the MagnaPure compact (Roche Diagnostics, Indianapolis, IN), and was eluted in 50 μl of which 5 μl was added to the GenMark RVP assay. At Memorial Healthcare System, respiratory virus samples were extracted utilizing the easyMag (bioMerieux, Durham, NC). Two-hundred microliters of sample (nasopharyngeal swab) collected and transported in viral transport medium was prepared using the on-board protocol and extracted as per manufacturer recommendations. Nasopharyngeal swab samples not placed in viral transport medium were occasionally collected in Liquid Stuarts media. These samples were processed in 2 ml of lysis buffer (bioMerieux, Durham, NC) and prepared in an off-board extraction protocol as per manufacturer recommendations before loading onto the easyMag extractor. Nucleic acid was eluted in 60 ul with 5 ul being used in the GenMark RVP assay. At BayCare Health System 200 μl of patient sample was extracted using the QIAGEN QIAamp MinElute Virus Spin Kit on the semi-automated QiaCube system with on-board lysis. Nucleic acid was eluted in 60 μl and 5 μl were used in the GenMark RVP assay.
Easymag
Manufactured by bioMérieux
Sourced in France, Canada, United States
The EasyMAG is a nucleic acid extraction system designed for automated and efficient extraction of DNA and RNA from a variety of sample types. It utilizes magnetic bead technology to isolate nucleic acids, providing a standardized and reliable sample preparation process. The EasyMAG is a versatile instrument suitable for use in clinical, research, and diagnostic laboratories.
Automatically generated - may contain errors
Lab products found in correlation
Magmax express 96, by Thermo Fisher Scientific (4 mentions)
Kingfisher flex, by Thermo Fisher Scientific (4 mentions)
Magna pure compact, by Roche (3 mentions)
Qiasymphony, by Qiagen (3 mentions)
Lysis buffer, by bioMérieux (2 mentions)
Magna pure lc 2, by Roche (2 mentions)
Superscript 4 reverse transcriptase, by Thermo Fisher Scientific (2 mentions)
Altostar purification kit 1, by Altona Diagnostics (2 mentions)
Abi 7500, by Thermo Fisher Scientific (2 mentions)
Stepone thermocycler, by Thermo Fisher Scientific (2 mentions)
Taqman universal master mix, by Thermo Fisher Scientific (2 mentions)
Taqpath 1 step rt qpcr master mix, by Thermo Fisher Scientific (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
Onestep rt pcr kit, by Qiagen (2 mentions)
Nuclisens easymag lysis buffer, by bioMérieux (2 mentions)
Turbo dnase, by Thermo Fisher Scientific (2 mentions)
Qiaamp minelute virus spin kit, by Qiagen (1 mentions)
Magmax viral pathogen 2 mvp 2 nucleic acid isolation kit, by Thermo Fisher Scientific (1 mentions)
Gs junior 454 sequencer, by Roche (1 mentions)
Gs flx titanium kit, by Roche (1 mentions)
63 protocols using easymag
1
Optimizing Viral RNA Extraction for GenMark RVP
2
RNA Extraction from Whole Blood and Urine
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Viral RNA from whole blood and urine samples was extracted using the easyMAG® automated extractor (BioMerieux, Quebec, Canada), according to manufacturer’s instructions.
3
Automated Viral RNA Extraction and qPCR
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For the TaqPath qPCR analysis, we used the MagMAX™ Viral/Pathogen II (MVP II) Nucleic Acid Isolation Kit for automated extraction (Thermo Fisher Scientific, AM1836) on 200 μl sample input. For internal control, samples were spiked with a purified MS2 bacteriophage as per the manufacturer’s instructions (Thermo Fisher Scientific, A47817). Extracted RNA was eluted from magnetic beads in 50 μl MagMAX Viral/Pathogen Elution Buffer.
For the multiplex respiratory panel, Total Nucleic Acid (TNA) extraction started from 500 µl of air sample in UTM with NucliSens extraction reagents on easyMAG or eMAG (BioMérieux, Lyon, France). We used the specific B protocol on the instrument after off-board lysis for 10 min and continuous shaking. A 10 μL mixture of Phocine Distemper Virus and Phocine Herpesvirus was added to the lysed sample before extraction as RNA and DNA internal controls46 (link),47 (link). The elution volume of TNA was 110 µl.
For the multiplex respiratory panel, Total Nucleic Acid (TNA) extraction started from 500 µl of air sample in UTM with NucliSens extraction reagents on easyMAG or eMAG (BioMérieux, Lyon, France). We used the specific B protocol on the instrument after off-board lysis for 10 min and continuous shaking. A 10 μL mixture of Phocine Distemper Virus and Phocine Herpesvirus was added to the lysed sample before extraction as RNA and DNA internal controls46 (link),47 (link). The elution volume of TNA was 110 µl.
4
SARS-CoV-2 Genomic Sequencing from Clinical Samples
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Patient samples were obtained from the Medical Universities of Vienna Institute of Virology, Medical University of Innsbruck Institute of Virology, Medical University of Innsbruck Department of Internal Medicine II, Central Institute for Medical-Chemical Laboratory Diagnostics Innsbruck, Klinikum Wels-Grieskirchen, and AGES. Samples were obtained from suspected or confirmed SARS-CoV-2 cases or contact persons of these. Sample types included oropharyngeal swabs, nasopharyngeal swabs, tracheal secretion, bronchial secretion, serum, plasma, and cell culture supernatants. RNA was extracted using the following commercially available kits by adhering to the manufacturers’ instructions: MagMax (Thermo Fisher Scientific), EasyMag (bioMérieux), AltoStar Purification Kit 1.5 (Altona Diagnostics), MagNA Pure LC 2.0 (Roche), MagNA Pure Compact (Roche), and QIAsymphony (Qiagen). Viral RNA was reverse transcribed with Superscript IV Reverse Transcriptase (Thermo Fisher Scientific). The resulting complementary DNA was used to amplify viral sequences with modified primer pools from the Artic Network initiative (43 (link)). Polymerase chain reactions were pooled and subjected to high-throughput sequencing.
5
Viral RNA Extraction from Clinical Samples
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Viral RNA from the different specimen types was extracted on one of three platforms using manufacturers’ instructions: easyMAG® (BioMerieux, Quebec, Canada) with associated reagents; the MagMAX Express 96 or KingFisher Flex automated extraction and purification systems (Thermo Fisher Scientific) with either the MagMAX™-96 Viral RNA Isolation Kit (ABI) or the Maxwell HT Viral TNA custom Kit (Promega); or the Hamilton STARlet automated extractor (Hamilton, Reno, NV, USA) with the Maxwell HT Viral TNA Custom Kit. The validated specimen types included throat swab, nasal swab, nasopharyngeal swab and aspirate, auger suction, bronchoalveolar lavage, endotracheal secretion, and lung tissue. The sample input and output volumes were 200 μl and 110 μl for all the respiratory sample types, respectively, and 60 μl and 200 μl for the tissue samples, respectively.
6
HIV Genetic Diversity Analysis Protocol
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HIV-1 RNA was extracted from plasma, seminal fluid, and saliva using the EasyMag (bioMérieux, Marcy l’Etoile, France) kit according to the manufacturer’s instructions. HIV-1 DNA was extracted from whole blood and non-spermatozoid cells using the QiaSymphony DSP DNA protocol « blood » (Qiagen, Courtaboeuf. France). The C2V3 env gene between positions 7008–7385 of the reference sequence HXB2 was amplified using the ANRS protocol (http://www.hivfrenchresistance.org/ANRS-procedures.pdf ). Amplicons were multiplexed and used for UDS on a Roche/454 GS. Amplicons were quantified, fixed onto microbeads, subjected to emulsion PCR, and the beads loaded onto picotiter plates for forward and reverse pyrosequencing by means of the GS-FLX Titanium Kit in a Roche 4.5.4 GS Junior sequencer (454 Life Sciences, Roche Diagnostics Corp., Brandford, Connecticut). HIV 8E5 cells harboring one copy of HIV per genome were sequenced as a control to establish the error cut off.
7
Amplicon-based NGS for Cancer Gene Profiling
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Genomic DNA was isolated by Qiagen DNA Micro kit (Qiagen, Hilden, Germany) or easyMAG (Biomérieux, Marcy I'Etoile, France) according to the manufacturer's instructions. Genomic DNA from frozen tissue specimens was subjected to amplicon‐based NGS using TruSeq Amplicon Cancer Panel (TSACP; Illumina, San Diego, CA, USA) and the MiSeq Personal Sequencer (Illumina), essentially as described before 14 . TSACP covers 212 amplicons from 48 cancer‐related genes, which are simultaneously amplified in a single‐tube reaction. A minimal variant allele frequency (VAF) of 0.05 was used to score mutations. High‐resolution melting followed by Sanger sequencing (HRM‐sequencing) for PIK3CA exon 9 was applied to genomic DNA from FFPE‐tissue specimens, as previously described 14 .
8
Respiratory Virus Diagnostic Protocol
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Samples were collected by patients’ health care provider with flocked swabs placed into 3-mL universal viral transport medium (Becton Dickinson). Nucleic acids were isolated from 0.2 mL of transport medium using the Nuclisens (Boom method) on the Easy Mag instrument (bioMerieux). DFA tests were performed using commercial reagents (Light Diagnostics SimulFluor Respiratory Screen Reagent, Millipore Corporation). PCR and direct fluorescent antigen testing for a panel of 9 respiratory viruses (Table 1 ) were performed as described previously [18–24 (link)].
9
Hydatid Cyst DNA Extraction Protocol
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Cystic liquid from hydatid cysts was collected and stored at −20°C until DNA extraction. DNA was extracted using a QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) following a modified procedure; an aliquot of 500 μl of specimens was centrifuged (1500g for 5 min), and the pellet was resuspended in 180 μl of QIAamp ATL buffer with 400 μg proteinase K and DNA extracted following the manufacturer recommendations and eluted from the kit columns to give a final volume of 100 μl [12 (link)].
EasyMag (bioMérieux, Italy) was used for automated extraction from 500 μl blood sample. DNA sample was eluted to a final volume of 55 μl.
EasyMag (bioMérieux, Italy) was used for automated extraction from 500 μl blood sample. DNA sample was eluted to a final volume of 55 μl.
10
Multiplex PCR for Respiratory Pathogens
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All samples were extracted using NucliSENS easyMag (BioMérieux Marcy-l’Étoile, France). Each extract was subjected to multiplex PCR using the FTD® Respiratory Pathogens 33 (FTD) method, which is an in vitro test with eight multiplex reverse-transcription (RT)-PCR reactions for the qualitative detection of the following viruses, bacteria, and fungi causing respiratory infections: influenza viruses A, B, and C; parainfluenza viruses 1, 2, 3, and 4; coronaviruses NL63, 229E, OC43, and HKU1; human metapneumoviruses A and B; rhinovirus; RSV A and B; adenovirus; enterovirus; parechovirus; bocavirus; cytomegalovirus; Pneumocystis jirovecii; M.pneumoniae; C.pneumoniae; S.pneumoniae; Haemophilus influenzae type B; S.aureus; Moraxella catarrhalis; Bordetella spp.; Klebsiella pneumoniae; Legionella spp.; Salmonella spp.; and H.influenzae. In total, 400 µL of each sample was extracted using easyMag®, based on the manufacturer’s instructions (BioMérieux, Marcy-l’Étoile, France). RT-PCR was run on Applied Biosystems ABI-7500 using the following conditions: 42 °C for 15 min, followed by 50 °C for 15 min, 94 °C for 3 min, and 95 °C for 10 min. Thereafter, the test was performed based on the following parameters: 40 cycles at 94 °C for 8 s and 40 cycles at 95 °C for 8 s, 60 °C for 34 s, and 60 °C for 34 s.
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