Genomiphi v2 dna amplification kit

Manufactured by GE Healthcare

Sourced in United Kingdom, United States, Sweden

The GenomiPhi V2 DNA Amplification Kit is a laboratory equipment product designed for the random amplification of genomic DNA. It is a commonly used tool in various molecular biology applications, including whole-genome amplification and DNA sample preparation.

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Lab products found in correlation

Qubit dsdna br assay, by Thermo Fisher Scientific (2 mentions) Trizol reagent, by Thermo Fisher Scientific (2 mentions) Dneasy blood and tissue kit, by Qiagen (2 mentions) Qiaamp dna mini kit, by Qiagen (2 mentions) Dnazol, by Molecular Research Center (2 mentions) Zymo ez dna methylation kit, by Zymo Research (2 mentions) Nanodrop 1000, by Thermo Fisher Scientific (2 mentions) Hiseq2000 dna sequencer, by Illumina (1 mentions) Lightcycler device, by Roche (1 mentions) Lightcycler probe design software 2, by Roche (1 mentions) Abi prism 7300 real time pcr system, by Thermo Fisher Scientific (1 mentions) Taqman snp genotyping assay, by Thermo Fisher Scientific (1 mentions) Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (1 mentions) Nucleospin tissue, by Macherey-Nagel (1 mentions) Dneasy tissue extraction kit, by Qiagen (1 mentions) Edta vacutainer, by BD (1 mentions) Luminex multi analyte profiling system xmap, by DiaSorin (1 mentions) Labtype sso hla dpa1 dpb1 kit, by Thermo Fisher Scientific (1 mentions) Nebnext ultra directional rna library prep kit, by New England Biolabs (1 mentions) 0.45 μm pore size membrane, by Merck Group (1 mentions)

41 protocols using genomiphi v2 dna amplification kit

Metagenomic DNA Amplification from Amerindian and Puerto Rican Samples

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We performed MDA on fecal and oral metagenomic DNA from Amerindian subjects 3, 5, 6, and 23 and the five Puerto Rican subjects with the illustra GenomiPhi V2 DNA Amplification Kit (GE Healthcare Life Sciences). The recommended protocol was followed with a 2-hour incubation. We pooled three to six reactions per sample to reduce MDA template amplification bias.

Clemente J.C., Pehrsson E.C., Blaser M.J., Sandhu K., Gao Z., Wang B., Magris M., Hidalgo G., Contreras M., Noya-Alarcón Ó., Lander O., McDonald J., Cox M., Walter J., Oh P.L., Ruiz J.F., Rodriguez S., Shen N., Song S.J., Metcalf J., Knight R., Dantas G, & Dominguez-Bello M.G. (2015). The microbiome of uncontacted Amerindians. Science Advances, 1(3), e1500183.

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Whole Genome Amplification of Tissue Punches

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We performed WGA on each punch using the illustra GenomiPhi V2 DNA Amplification kit (GE Healthcare Life Sciences). Punches were transferred in 0.2 mL sterile tubes using a sterile tip. We performed reactions following the manufacturer’s instructions, immersing each punch in 9 μL of sample buffer and keeping tubes on ice at all times after the denaturation step. After amplification, we quantified DNA using the Qubit dsDNA BR assay (Invitrogen, USA).

Chevalier F.D., Le Clec’h W., Eng N., Rugel A.R., de Assis R.R., Oliveira G., Holloway S.P., Cao X., Hart P.J., LoVerde P.T, & Anderson T.J. (2016). Independent origins of loss-of-function mutations conferring oxamniquine resistance in a Brazilian schistosome population. International journal for parasitology, 46(7), 417-424.

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Metagenomic Sequencing of Hot Spring Soil

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The soil sample was collected by scratching the surface of a spout of a hot spring (70 °C and pH 7.2 when sampled) by a spatula in the Onikobe-onsen-kyo geothermal area at lat. 38˚48’ and at long. 140˚40’ (Miyagi, Japan) in June, 2009. Metagenomic DNA was extracted from microbes in 10 g of the soil using an ISOIL Large for Beads, ver. 2, DNA extraction kit (Nippon Gene, Tokyo, Japan). Five micrograms of the extracted DNA were sequenced using a GS FLX Titanium DNA sequencer (Roche Diagnostics, Basel, Switzerland) according to the supplier’s protocol. In addition, the genomic DNA was amplified using a GenomiPhi V2 DNA amplification kit (GE Healthcare, Little Chalfont, UK) and then sequenced using a Hiseq 2000 DNA sequencer (Illumina, San Diego, CA, USA) according to the supplier’s protocol. Sequences with a total length of 1.11 Gbp and average length of 396 bp for each read were obtained from the former sequence, and sequences with a total length of 83.1 Gbp and average length of 92.7 bp for each read were obtained from the latter sequence. Uncertain sequences were trimmed from the raw sequences based on the quality score defined, and the resulting sequences were used for de novo assembly using CLC Genomics Workbench software, ver. 4.0.

Sato M., Suda M., Okuma J., Kato T., Hirose Y., Nishimura A., Kondo Y, & Shibata D. (2017). Isolation of highly thermostable β-xylosidases from a hot spring soil microbial community using a metagenomic approach. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 24(6), 649-656.

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Metagenomic DNA Amplification from Amerindian and Puerto Rican Samples

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Genetic Screening of PROCR Locus in Ghanaians

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In order to screen the PROCR locus on chromosome 20 (chr20: 33,758,824–33,765,355) for genetic variants, DNA from 3,771 unrelated Ghanaian individuals (1,905 SM cases and 1,866 healthy controls) was used for HRM. Prior to the screen, genomic DNA had been whole-genome amplified by Genomiphi V2 DNA amplification kit (GE Healthcare). DNA samples were then amplified by PCR using primers that captured 1,100 bp upstream of the transcription start site, exons and their flanking regions, and 750 bp of the 3′-UTR. Oligonucleotides were designed using LightCycler Probe Design Software 2.0 (Roche Applied Science) against reference transcript NCBI NM_006404. Sequences of oligonucleotides and PCR conditions for HRM assays are listed in S1 Table. Previously unknown SNPs and singletons were confirmed by re-sequencing genomic DNA. In addition, 13 variants detected by HRM were genotyped by allele-specific hybridization in a Roche LightCycler device (S2 Table).

Schuldt K., Ehmen C., Evans J., May J., Ansong D., Sievertsen J., Muntau B., Ruge G., Agbenyega T, & Horstmann R.D. (2014). Endothelial Protein C Receptor Gene Variants Not Associated with Severe Malaria in Ghanaian Children. PLoS ONE, 9(12), e115770.

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Genomic DNA Extraction and SNP Genotyping

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gDNA was extracted using the wizard SV 96 genomic DNA purification system (Promega, Leiden, The Netherlands). In case of a low yield, pre-amplification of gDNA was performed with the GenomiPhi V2 DNA Amplification Kit (GE Healthcare, Diegem, Belgium). 10 ng of gDNA was used in Taqman SNP genotyping assays (Applied Biosystems, Life Technologies, Merelbeke, Belgium) for SNPs rs301, rs328 and rs13702 on an ABI Prism 7300 Real Time PCR System (Applied Biosystems, Life Technologies).

Rombout A., Stamatopoulos B., Lagneaux L., Lust S., Offner F., Naessens E., Vanderstraeten H., Verhasselt B, & Philippé J. (2015). Lipoprotein Lipase SNPs rs13702 and rs301 Correlate with Clinical Outcome in Chronic Lymphocytic Leukemia Patients. PLoS ONE, 10(3), e0121526.

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DNA Extraction and Amplification Methods

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For cohort 1, DNA was extracted using DNeasy Blood and Tissue kit (Qiagen) as previously described (O'Brien et al., 2014 (link)). For cohort 2, DNAs were extracted using QIAamp DNA mini kit (QIAgen) according to standard protocols. For the third cohort, DNA extraction was performed from specimens preserved in RNAlater, using Trizol reagent (Invitrogen life technologie) with NucleoSpin Tissue (Macherey-Nagel).
DNA quantity and quality were checked for all samples using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, USA). Of the total of 509 DNA samples, 39 with DNA concentrations less than 20 ng/μl were removed. DNA samples were pre-amplified using the GenomiPhi V2 DNA Amplification kit (GE Healthcare) according to the manufacturer's instructions. Briefly, 25 ng of each DNA sample was heat-denatured at 95°C. After addition of the enzyme solution, the sample was incubated at 30°C for 90 min. DNA polymerases were then heat-inactivated at 65°C for 10 min and samples were stored at −20°C until use.

Le Baut G., O'Brien C., Pavli P., Roy M., Seksik P., Tréton X., Nancey S., Barnich N., Bezault M., Auzolle C., Cazals-Hatem D., Viala J., Allez M., Hugot J.P, & Dumay A. (2018). Prevalence of Yersinia Species in the Ileum of Crohn's Disease Patients and Controls. Frontiers in Cellular and Infection Microbiology, 8, 336.

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Blood Collection and DNA Extraction for Rectal Cancer

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Blood was collected in EDTA-vacutainers (BD, Franklin Lakes, NJ) from patients with rectal cancer who underwent pre-neoadjuvant chemoradiation and stored at 4°C until further use. Genomic DNA was extracted from whole blood samples from using Qiagen® DNeasy Tissue Extraction Kit (Valencia, CA). Whole genome amplification of each sample was performed using the illustra GenomiPhi V2 DNA Amplification Kit (GE Healthcare, Pittsburgh, PA). DNA concentration was determined after whole genome amplification using spectrophotometry.

Nelson B., Carter J.V., Eichenberger M.R., Netz U, & Galandiuk S. (2016). Genetic polymorphisms in 5-FU related enzymes predict pathologic response following neoadjuvant chemoradiation for rectal cancer. Surgery, 160(5), 1326-1332.

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DNA Sample Preparation and Whole Genome Amplification

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The 104 DNA samples from our lab collection were obtained from peripheral blood, saliva or cultured cells. Target sequencing required specific quality and quantity parameters for the DNA to be analysed: 1) absence or low amount of DNA degradation; 2) quantity ≥ 3 μg; 3) concentration ≥ 37.5 ng/μl; 4) purity, A260/280 = 1.8–2.0. Concentration and purity were measured using a NanoDrop 1000 spectrophotometer, produced by Thermo Fisher Scientific. Degradation was assessed by means of an electrophoretic run on a 1 % agarose gel. We performed a whole genome amplification (WGA) of 59 samples with an insufficient quantity of DNA, using the GenomiPhi V2 DNA Amplification kit (GE Healthcare) according to the manufacturer’s protocol.

D’Atanasio E., Trombetta B., Bonito M., Finocchio A., Di Vito G., Seghizzi M., Romano R., Russo G., Paganotti G.M., Watson E., Coppa A., Anagnostou P., Dugoujon J.M., Moral P., Sellitto D., Novelletto A, & Cruciani F. (2018). The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages. Genome Biology, 19, 20.

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High-Resolution HLA Genotyping in Asia

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High resolution (4-digit) genotyping of HLA-DPA1 and -DPB1 alleles was performed for HBV patients, resolved individuals, and healthy controls in Japan, Korea, Hong Kong, and Thailand. LABType SSO HLA DPA1/DPB1 kit (One Lambda, CA) and a Luminex Multi-Analyte Profiling system (xMAP; Luminex, Austin, TX) were used for genotyping, in according with the manufacturer's protocol. Because of the small quantity of genomic DNA in some Korean samples, we performed whole genome amplification for a total of 486 samples using GenomiPhi v2 DNA Amplification kit (GE Healthcare Life Sciences, UK), in accordance with the manufacturer's instruction.
A total of 2,895 samples were successfully genotyped and characteristics of these samples are summarized in Table S1.

Nishida N., Sawai H., Kashiwase K., Minami M., Sugiyama M., Seto W.K., Yuen M.F., Posuwan N., Poovorawan Y., Ahn S.H., Han K.H., Matsuura K., Tanaka Y., Kurosaki M., Asahina Y., Izumi N., Kang J.H., Hige S., Ide T., Yamamoto K., Sakaida I., Murawaki Y., Itoh Y., Tamori A., Orito E., Hiasa Y., Honda M., Kaneko S., Mita E., Suzuki K., Hino K., Tanaka E., Mochida S., Watanabe M., Eguchi Y., Masaki N., Murata K., Korenaga M., Mawatari Y., Ohashi J., Kawashima M., Tokunaga K, & Mizokami M. (2014). New Susceptibility and Resistance HLA-DP Alleles to HBV-Related Diseases Identified by a Trans-Ethnic Association Study in Asia. PLoS ONE, 9(2), e86449.

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