Ez1 advanced

Manufactured by Qiagen

Sourced in Spain, Germany

The EZ1 Advanced is a compact, automated sample preparation system designed for nucleic acid extraction. It utilizes magnetic-bead based technology to efficiently purify DNA, RNA, or viral nucleic acids from a variety of sample types. The system provides a standardized, consistent workflow to streamline the sample preparation process.

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Lab products found in correlation

Ez1 tissue kit, by Qiagen (2 mentions) 16s metagenomics sequencing library preparation protocol, by Illumina (2 mentions) Dneasy powerclean cleanup kit, by Qiagen (2 mentions) Nextera xt kit, by Illumina (2 mentions) Ez1 dna tissue kit, by Qiagen (2 mentions) Quantifiler human dna quantification kit, by Thermo Fisher Scientific (2 mentions) Microcavitation, by Covaris (2 mentions) Nuclisens easymag, by bioMérieux (1 mentions) Quantstudio 12k flex, by Thermo Fisher Scientific (1 mentions) Taqman genotyper software, by Thermo Fisher Scientific (1 mentions) Paraquat, by Merck Group (1 mentions) Ez1 rna universal tissue kit, by Qiagen (1 mentions) Tissuelyser 2, by Qiagen (1 mentions) Qiazol lysis reagent, by Qiagen (1 mentions) Flex purification system, by Thermo Fisher Scientific (1 mentions) Magmax viral pathogen 2 nucleic acid isolation kit, by Thermo Fisher Scientific (1 mentions) Magna pure compact, by Roche (1 mentions) Qiaamp viral rna mini kit, by Qiagen (1 mentions)

13 protocols using ez1 advanced

Microbiome DNA Extraction and Sequencing

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Whole stool samples were stored at −80°C until DNA extraction. Prepped samples were loaded on the EZ1 Advanced (Qiagen, Valencia, CA) using the EZ1 Tissue Kit and the Bacterial DNA Extraction protocol card. Samples were cleaned and concentrated using the DNeasy PowerClean Cleanup kit (Qiagen, Valencia, CA).
Sequencing libraries were prepared using a Nextera XT kit (Illumina, San Diego, CA) using a modified Illumina 16S Metagenomics Sequencing Library Preparation protocol for analysis of hypervariable region V4. Each sample was sequenced on the Illumina MiSeq with paired-end reads of 301bp. Sequencing of negative controls of lysis buffer and positive controls of Staphylococcus aureus (Strain NCTC 8532, ATCC, VA) and Escherichia coli (Strain NCTC 9001, ATCC, VA) were included. The sequence data are being deposited in NCBI Sequence Read Archive (SRA).

Hourigan S.K., Moutinho TJ J.r., Berenz A., Papin J., Guha P., Bangiolo L., Oliphant S., Provenzano M., Baveja R., Baker R., Vilboux T., Levy S., Deopujari V., Nataro J.P., Niederhuber J.E, & Moore S.R. (2020). Gram-negative microbiota blooms in premature twins discordant for parenteral nutrition associated cholestasis. Journal of pediatric gastroenterology and nutrition, 70(5), 640-644.

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Automated DNA Extraction Protocol for Bacterial Samples

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DNA extractions were performed using the Qiagen EZ1 Advanced automated extraction platform (Qiagen Inc., Valencia, CA) with the bacterial card and tissue extraction kit. All sample manipulation was done in the BSL2 hood with appropriate laminar flow. Frozen samples were thawed at 4°C and vortexed to ensure mixing. An aliquot of 200 μl for extraction was transferred into the tube provided with the EZ1 kit. Remaining sample was stored at -70 C. Extraction reagent cartridges, elution tubes and tip holders were loaded into the EZ1 sample rack as instructed by the manufacturer. Elution volume of 100μl was selected and EZ1 DNA Tissue Kit program was run. Elution tubes with DNA extract were stored at -20°C. DNA extraction reagents were confirmed free of bacterial DNA by performing control extractions utilizing buffer or PCR grade water. Total bacterial load was measured using a quantitative real-time PCR assay that has been previously published [27 (link), 28 (link)].

Wagner B.D., Sontag M.K., Harris J.K., Miller J.I., Morrow L., Robertson C.E., Stephens M., Poindexter B.B., Abman S.H, & Mourani P.M. (2017). Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants. PLoS ONE, 12(1), e0170120.

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Automated Bacterial DNA Extraction

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DNA extractions were performed using the Qiagen EZ1 Advanced automated extraction platform (Qiagen Inc., Valencia, CA) with the bacterial card and tissue extraction kit. Details of the DNA extraction are available in the online supplement. Total bacterial load was measured using a quantitative real-time PCR assay that has been previously published.[10 ]

Wagner B.D., Sontag M.K., Harris J.K., Miller J.I., Morrow L., Robertson C.E., Stephens M.J., Poindexter B.B., Abman S.H, & Mourani P.M. (2017). Prenatal Complications Are Associated with the Postnatal Airway Host Response and Microbiota in Intubated Pre-term Infants. The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians, 32(9), 1499-1506.

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Automated Bacterial DNA Extraction Protocol

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Automated Nucleic Acid (NA) extractions were carried out from fresh well-isolated colonies by NuclisensEasyMAG (bioMerieux, France) or by EZ1 advanced (Qiagen, Germany) using EZ1^™ DNA Tissue Kit according to the protocol recommended by the manufacturers. Briefly, from bacterial colonies: a 2.0 McFarland-standard bacterial suspension was prepared from isolated colonies in saline, and bacterial NA was extracted from 200 μl (1.2 X10⁸ CFU) of the suspension. Extracted bacterial NA was eluted from the columns in 100 μl elution buffer and stored at -20°C.

Meir-Gruber L., Manor Y., Gefen-Halevi S., Hindiyeh M.Y., Mileguir F., Azar R., Smollan G., Belausov N., Rahav G., Shamiss A., Mendelson E, & Keller N. (2016). Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples. PLoS ONE, 11(10), e0164873.

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DNA Extraction from Paraffin Samples

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DNA was isolated from archival samples using the Qiagen EZ1 Advanced using magnetic bead technology, with the “purification of DNA from paraffin-embedded tissue” protocol, the EZ1 DNA Tissue Kit, and the EZ1 DNA Paraffin card. The purified DNA was quantified by the Quantifiler by Life Technologies and purity based on the inhibition of polymerase chain reaction.

Vaishampayan U., Shevrin D., Stein M., Heilbrun L., Land S., Stark K., Li J., Dickow B., Heath E., Smith D, & Fontana J. (2015). Phase II Trial of Carboplatin, Everolimus, and Prednisone in Metastatic Castration-resistant Prostate Cancer Pretreated With Docetaxel Chemotherapy: A Prostate Cancer Clinical Trial Consortium Study. Urology, 86(6), 1206-1211.

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Quantitative BALF DNA Extraction Protocol

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DNA extractions were performed on 0.2 μL BALF using the Qiagen EZ1 Advanced automated extraction platform (Qiagen, Valencia, CA, USA). Total bacterial load (TBL) was measured using a quantitative real-time PCR assay [29 (link)]. A dilution factor was applied to convert results to gene copies per millilitre. Reagent controls were analysed to determine background bacterial load and to estimate the limit of detection (LOD; defined as mean TBL_Controls+(3.3×SD_Controls)) for TBL assay. TBL values below the LOD were recorded, but LOD is shown in the relevant figures.

Zemanick E.T., Wagner B.D., Robertson C.E., Ahrens R.C., Chmiel J.F., Clancy J.P., Gibson R.L., Harris W.T., Kurland G., Laguna T.A., McColley S.A., McCoy K., Retsch-Bogart G., Sobush K.T., Zeitlin P.L., Stevens M.J., Accurso F.J., Sagel S.D, & Harris J.K. (2017). Airway microbiota across age and disease spectrum in cystic fibrosis. The European respiratory journal, 50(5), 1700832.

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DNA Extraction from Dried Blood Spots

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DNA was isolated from dried blood spots with Qiagen (Hilden, Germany) EZ1 Advanced^® using the DNA Investigator^® reagents and protocol card. The ‘Stains on Fabric’ preprocessing and Trace^® (tip-dance) instrument protocol was used for isolation. The Quantifiler Human DNA Quantification Kit^® (Applied Bio-systems, Inc., MA, USA) was used to determine the amount of amplifiable DNA.
Approximately 3 μg genomic DNA was diluted in 130 μl of buffer TE (10 mM Tris [pH 8.0], and 1 mM EDTA [pH 8.0]) and sheared into ~200–600 bp fragments using microcavitation (Covaris, Inc, MA, USA) setting: Duty Cycle = 5%, intensity = 3, cycles/burst = 200, time = 75 s run at 6–8°C). A 125 μl of the sheared DNA samples were mixed with 330 μl of buffer TE. The sheared DNA was denatured by boiling it in the Thermomixer at 95°C and 700 rpm for 10 min and left on ice for 10 min.

Sen A., Heredia N., Senut M.C., Hess M., Land S., Qu W., Hollacher K., Dereski M.O, & Ruden D.M. (2015). Early life lead exposure causes gender-specific changes in the DNA methylation profile of DNA extracted from dried blood spots. Epigenomics, 7(3), 379-393.

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DNA Isolation and Fragmentation for Sequencing

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DNA was isolated from dried blood spots with Qiagen EZ1 Advanced® using the DNA Investigator® reagents and protocol card. The “Stains on Fabric” preprocessing and Trace® (tip-dance) instrument protocol was used for isolation. The Quantifiler Human DNA Quantification Kit® (Applied Biosystems, Inc.) was used to determine the amount of amplifiable DNA. Approximately 3 μg genomic DNA was diluted in 130 μl of buffer TE (10 mM Tris (pH 8.0), and 1 mM EDTA (pH 8.0)) and sheared into ~200–600 bp fragment using microcavitation (Covaris, Inc, setting: Duty Cycle = 5%, Intensity = 3, Cycles/burst = 200, Time = 75 seconds run at 6–8 °C). 125 μl of the sheared DNA samples were mixed with 330 μl of buffer TE. The sheared DNA was denatured by boiling it in the Thermomixer at 95 °C and 700 rpm for ten minutes and left on ice for 10 min.

Sen A., Heredia N., Senut M.C., Land S., Hollocher K., Lu X., Dereski M.O, & Ruden D.M. (2015). Multigenerational epigenetic inheritance in humans: DNA methylation changes associated with maternal exposure to lead can be transmitted to the grandchildren. Scientific Reports, 5, 14466.

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BDNF Val66Met Polymorphism Analysis

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Genetic analyses were carried out at the WSU Applied Genomics Technology Center. DNA was isolated from saliva collected in Oragene DNA collection tubes using EZ1 Advanced (Qiagen) with standard conditions. The BDNF Val66Met polymorphism (rs6265) was investigated using a 5′-nuclease assay (Life Technologies TaqMan assay C_11592758_10). Assays were run in a 5 microliter reaction under standard TaqMan conditions on a QuantStudio 12K Flex (Life Technologies). Data were analyzed using Taqman Genotyper software (v.1.3; Life Technologies).

Marusak H.A., Kuruvadi N., Vila A.M., Shattuck D.W., Joshi S.H., Joshi A.A., Jella P.K, & Thomason M.E. (2015). Interactive effects of BDNF Val66Met genotype and trauma on limbic brain anatomy in childhood. European child & adolescent psychiatry, 25(5), 509-518.

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Paraquat-Induced Stress Response in S2 Cells

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S2 cells were subjected to RNAi alone or RNAi and 24 h treatment with 8.3 mM paraquat (1,1′-dimethyl-4,4′-bipyridinium dichloride (Sigma Aldrich)). Total RNA was isolated using the EZ1^® RNA Universal Tissue Kit (Qiagen). Cells were disrupted and homogenized in 750 µl QIAzol™ lysis reagent via bead-milling on the TissueLyser^® II (Qiagen). RNA was collected from the homogenate by chloroform extraction and purified on the EZ1^® Advanced (Qiagen) with additional DNase step to remove any residual DNA. Purified total RNA was quantified by UV spectrophotometry using the DropSense96^® Microplate Spectrophotometer (Trinean) and purity was assessed based on the A260/A280 and A260/A230 ratios. RNA quality was assessed by microfluidics using the RNA R6K assay for the Agilent 2200 TapeStation. The electrophoretogram was examined to determine overall quality of the RNA.

Gajan A., Barnes V.L., Liu M., Saha N, & Pile L.A. (2016). The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3. Epigenetics & Chromatin, 9, 4.

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