Genomic dna analysis screentape

Manufactured by Agilent Technologies

Sourced in United States

The Genomic DNA Analysis ScreenTape is a lab equipment product from Agilent Technologies that is used for the analysis of genomic DNA samples. It provides a rapid and automated solution for the assessment of DNA quality and quantity.

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7 protocols using genomic dna analysis screentape

Bonamia Specificity Assessment via LAMP

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Specificity of the LAMP assays was evaluated by testing samples infected with B. ostreae or B. exitiosa originating from different geographic sites for assessing test inclusivity (to make sure the assay would not miss some targeted parasites) and with closely related parasites for assessing exclusivity (to make sure the assay would not amplify parasites other than parasites of the genus Bonamia). Additionally, a selection of LAMP products was examined with TapeStation Analysis Software A.02.02 using the Genomic DNA screen tape analysis (Agilent Technologies) to visualize the appearance of primer dimmers or other artefacts.

Cano I., Wood G., Stone D., Noyer M., Canier L, & Arzul I. (2024). Loop-Mediated Isothermal Amplification for the Fast Detection of Bonamia ostreae and Bonamia exitiosa in Flat Oysters. Pathogens, 13(2), 132.

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Exome Sequencing of Family Members

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Blood samples were initially collected from the participants and DNA was prepared as previously described (Svensson et al. 2011 (link)). We re-measured available DNA concentration of available genomic DNA from family members using Qubit BR dsDNA assay (Life Technologies, USA). Individuals III:2, IV:1, IV:5, IV:6, IV:7, IV:9, IV:11, V:6, V7 and V:8 were selected for exome sequencing (Fig. 1a). All DNA samples used for exome sequencing were tested for DNA degradation using Genomic DNA ScreenTape analysis (Agilent Technologies, USA). Subsequently, 100 ng non-degraded genomic DNA per sample was used in AmpliSeq library preparations followed by Ion Proton (Life Technologies, USA) sequencing at the Science for Life Laboratory, Uppsala, Sweden, according to standard protocols. AmpliSeq target regions are available upon request. The Ion Proton sequencing was performed on P1 chips producing 200-bp sequence reads.

Einarsdottir E., Svensson I., Darki F., Peyrard-Janvid M., Lindvall J.M., Ameur A., Jacobsson C., Klingberg T., Kere J, & Matsson H. (2015). Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family. Human Genetics, 134, 1239-1248.

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Amplicon-based Metagenomic Sequencing Protocol

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Library preparation and sequencing were performed by Admera Health (South Plainfield, NJ, USA). Isolated genomic DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Waltham, MA, USA) and DNA quality was evaluated by Genomic DNA ScreenTape analysis (Agilent Technologies, Santa Clara, CA, USA). Library preparation was performed using Nextera XT library kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations while barcoding was performed using Illumina 8-nt dual-indices. The final library was evaluated by Qubit 2.0 DNA HS Assay and the quality of the library generated was examined by TapeStation HSD1000 ScreenTape (Agilent Technologies). Final library quantity was measured by KAPA SYBR FAST qPCR with QuantStudio 5 System (Applied Biosystems, Waltham, MA, USA). Equimolar pooling of libraries was performed based on qPCR QC values before sequencing on an Illumina HiSeq with a read length configuration of 2 × 150 paired end reads, obtaining 1 M PE reads per sample.

Gioia G., Severgnini M., Cremonesi P., Castiglioni B., Freeman J., Sipka A., Santisteban C., Wieland M., Gallardo V.A., Scott J.G., Moroni P, & Addis M.F. (2023). Genomic Characterization of Mycoplasma arginini Isolated from a Housefly on a Dairy Farm and Comparison with Isolates from Bovine Milk and Lung Tissue. Microbiology Spectrum, 11(3), e03010-22.

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Tumor sample preparation and nucleic acid extraction

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Snap frozen samples were sectioned and embedded in OCT. Frozen section slides were cut on a cryostat with a section depth of 5um, stained with hematoxylin and eosin. Diagnosis was confirmed and all samples were reevaluated for cellular content and quality by a pathologist (F.K.H. or S.J.C). After visual inspection, samples with > 70% tumor were macrodissected from the OCT block at a depth of up to 5mm for library preparation. Samples were disrupted with a mortar and pestle under liquid nitrogen and homogenized with a QIAshredder (QIAgen, 79654). DNA and RNA were extracted using the AllPrep kit (QIAgen, 80204). Germline DNA (peripheral blood) was extracted using DNeasy Blood and Tissue kit (Qiagen, 69504) according to manufacturer’s instructions. DNA was quantified using the Nanodrop 2000c (Thermo Fisher) and the QuBit High Sensitivity dsDNA assay (Thermo Fisher, Q32851). DNA integrity was quantified using the Genomic DNA Analysis ScreenTape (Agilent, 5067–5365) on the TapeStation 4200 (Agilent). RNA was quantified using Nanodrop 200c (Thermo Fisher) and QuBit High Sensitivity RNA assay (Thermo Fisher, Q32852). RNA was quantified using High Sensitivity RNA ScreenTape (Agilent, 5067–5579) on a TapeStation 4200 (Agilent).

Sayles L.C., Breese M.R., Koehne A.L., Leung S.G., Lee A.G., Liu H.Y., Spillinger A., Shah A.T., Tanasa B., Straessler K., Hazard F.K., Spunt S.L., Marina N., Kim G.E., Cho S.J., Avedian R.S., Mohler D.G., Kim M.O., DuBois S.G., Hawkins D.S, & Sweet-Cordero E.A. (2018). Genome-Informed Targeted Therapy for Osteosarcoma. Cancer discovery, 9(1), 46-63.

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Shotgun Metagenomic Profiling of Piglet Gut Microbiome

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Total genomic DNA was extracted from colon digesta of n = 6 piglets/group using the QIAamp Fast DNA Stool Mini Kit (Qiagen, Hilden, Germany). After DNA quality control using the Genomic DNA Analysis ScreenTape on a 2200 TapeStation Instrument (Agilent Technologies) and concentration measurement using the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific), shotgun metagenomic libraries were generated using the Nextera DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. Libraries were quality-controlled using the D5000 DNA Analysis ScreenTape on a 2200 TapeStation Instrument (Agilent Technologies), and sequenced on an Illumina NextSeq500 with 2 × 150 bp. Finally, sequencing reads were demultiplexed based on the used Nextera indices (dual indexing principle).

Pieper R., Dadi T.H., Pieper L., Vahjen W., Franke A., Reinert K, & Zentek J. (2020). Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire. The ISME Journal, 14(11), 2783-2793.

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Illumina Sequencing of Sheared Genomic DNA

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Genomic DNA (10 ng) was sheared in an M220 Focused-ultrasonicator™ (Covaris Inc., Woburn, MA) using settings for an average fragment of 300, 500, or 700 base pairs. Genomic libraries were constructed for Illumina sequencing using Ovation^® Ultralow Library Systems V2 (NuGEN Technologies Inc., San Carlos, CA) [22 (link)]. Libraries were barcoded to facilitate pooling during subsequent sequencing runs. Size distribution and concentration of genomic DNA libraries were analyzed by electrophoresis using Genomic DNA Analysis ScreenTape and D1000 ScreenTape on a 2200 TapeStation (Agilent). Barcoded genomic DNA libraries were pair-end sequenced using Illumina MiSeq Reagent v3 (600 cycles, 2 × 300 bp) kits (Illumina Inc., San Diego, CA).

Qvarnstrom Y., Wei-Pridgeon Y., Van Roey E., Park S., Srinivasamoorthy G., Nascimento F.S., Moss D.M., Talundzic E, & Arrowood M.J. (2018). Purification of Cyclospora cayetanensis oocysts obtained from human stool specimens for whole genome sequencing. Gut Pathogens, 10, 45.

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Target Capture and Paired-End Sequencing

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Target capture was performed according to the manufacturer’s protocol using the SureSelect XT automation reagent kit (Agilent, Santa Clara, CA), and a paired-end sequencing library was prepared using a barcode. The size and quality of the genomic DNA were validated using the Genomic DNA Analysis ScreenTape and Genomic DNA Reagent together with the Agilent 4200 Tape station (Agilent). Libraries were sequenced using the TG NextSeq 500/550 High Output Kit v2 (Illumina, Inc., San Diego, CA) and TG NextSeq 500/550 Mid Output Kit v2 (Illumina, Inc.).

Lee H., Lee B., Kim D.G., Cho Y.A., Kim J.S, & Suh Y.L. (2021). Detection of TERT Promoter Mutations Using Targeted Next-Generation Sequencing: Overcoming GC Bias through Trial and Error. Cancer Research and Treatment : Official Journal of Korean Cancer Association, 54(1), 75-83.

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