On request of a small farm in Kibaale district in Uganda, 20 whole blood samples of suspected ASF domestic pigs were screened at Makerere University (Kampala, Uganda). DNA was extracted using a Quick-gDNATM MiniPrep kit from ZYMO Research (Irvine, CA, United States) according to the manufacturer’s instructions. For the heating/lysis buffer method, samples were incubated with 200 µL genomic lysis buffer from the Miniprep kit at 70 °C for 20 min. RPA was performed as mentioned above.
Quick gdna miniprep kit
Manufactured by Zymo Research
Sourced in United States, Germany
The Quick-gDNA MiniPrep kit is a laboratory product designed for the rapid isolation of high-quality genomic DNA from a variety of sample types. The kit utilizes a simple, spin-column based protocol to efficiently extract and purify DNA from cells or tissues.
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Lab products found in correlation
Ez dna methylation gold kit, by Zymo Research (8 mentions)
Ez dna methylation lightning kit, by Zymo Research (4 mentions)
Wizard genomic dna purification kit, by Promega (4 mentions)
Qubit dsdna broad range assay, by Thermo Fisher Scientific (3 mentions)
Qubit 2.0 fluorometer, by Thermo Fisher Scientific (3 mentions)
Dneasy blood and tissue kit, by Qiagen (3 mentions)
Phusion high fidelity pcr master mix, by Thermo Fisher Scientific (3 mentions)
Rapid dna ligation kit, by Thermo Fisher Scientific (3 mentions)
Q5 high fidelity dna polymerase, by New England Biolabs (3 mentions)
Dreamtaq green pcr master mix, by Thermo Fisher Scientific (3 mentions)
Purelink genomic dna mini kit, by Thermo Fisher Scientific (3 mentions)
Nd 1000 spectrophotometer, by Thermo Fisher Scientific (3 mentions)
Qubit 3.0 fluorometer, by Thermo Fisher Scientific (3 mentions)
5 mc dna elisa kit, by Zymo Research (2 mentions)
Infinium humanmethylation450 beadchip platform, by Illumina (2 mentions)
Dna clean concentrator 5 kit, by Zymo Research (2 mentions)
Minelute reaction kit, by Qiagen (2 mentions)
Pan monocyte isolation kit, by Miltenyi Biotec (2 mentions)
Aria 2 cell sorter, by BD (2 mentions)
Pjet 1.2 pcr cloning vector, by Thermo Fisher Scientific (2 mentions)
151 protocols using quick gdna miniprep kit
1
ASF Screening in Ugandan Pigs
2
Genetic Characterization of ESBL-Klebsiella
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Total DNA from all ESBL-Kp was extracted using the Quick-gDNA TM MiniPrep kit (ZYMO RESEARCH Corp., USA). Detection by PCR of beta-lactamase (bla) genes encoding KPC-, VIM-, TEM-, OXA- and CTX-M-type enzymes was performed, as described previously [14 (link)]. The intrinsic SHV-1 and SHV-5-type enzymes were differentiated by PCR, as described previously [15 (link)]. Sequences of the PCR products were determined in both strands. Production of the respective beta-lactamases was confirmed by isoelectric focusing (IEF) [14 (link)]. The presence of the fimH, ugeE, wabG, ureA, magA, allS and rmpA virulence genes was assessed by PCR, as described previously [16 (link)].
3
DNA Isolation from Tissue and Cells
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Total DNA was isolated from tissue and cultured cells using the Quick-gDNATM MiniPrep kit (Zymo Research Corporation, Irvine, CA, USA) following the manufacturer’s instructions. DNA concentration was determined using the Qubit 2.0 fluorimeter (Life Technologies Corporation, Carlsbad, CA, USA).
4
Quantification of Global DNA Methylation
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Total genomic DNA from blood samples of the animals were isolated and analyzed for 5-methylcytidine, as described previously by our group, using the Quick-gDNATM MiniPrep kit from Zymo research (Irvine, CA, United States). After quantification, an equal amount of genomic DNA was used to estimate global levels of 5-methylcytosine using 5-mC DNA ELISA kit from Zymo research (Irvine, CA, United States) by following the manufacturer’s instructions as described earlier by our group (Narayanan et al., 2014 (link); Veeranki et al., 2015 (link)).
5
KIR Genotyping from Blood Samples
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Genomic DNA was isolated from PBMC or whole blood at the University of Zimbabwe College of Health Sciences, Harare, Zimbabwe using the Quick-gDNA TM MiniPrep kit (Zymo Research Corporation, Irvine, CA, USA) according to the manufacturer's instructions. KIR genotyping was carried out at the University of Oxford, Oxford, United Kingdom using sequence specific primer polymerase chain reaction (SSP-PCR) according to a previously described method (Martin and Carrington, 2008) . Briefly, two pairs of sequence specific primers were used to amplify each of 14 functional KIR genes; 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 3DS1, 3DL1, 3DL2, 3DL3 and the pseudogene 2DP1. The ethidium bromide stained amplicons were electrophoresed on 2% agarose gel and visualized under ultraviolet light for determination of presence/absence of each gene. The allelic variants of the KIR2DS4 gene were also determined by gel electrophoresis since the deleted version of the gene (KIR2DS4v) is 22 base pairs (bp) shorter in length than the full gene (KIR2DS4v).
6
Human PlGF Promoter Cloning
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Human genomic DNA was extracted from BEAS-2B by a Quick-gDNA MiniPrep kit (Zymo Research, CA, USA). The 2.0 kb human PlGF promoter region was amplified from human genomic DNA using polymerase chain reaction (PCR) performed with Hi Fi Taq DNA polymerase (Geneaid, Taipei, Taiwan) as follows: 2 minutes at 94°C, then 15 sec at 94°C, 30 sec at 59°C, and 2 min and 30 sec at 72°C for 35 cycles. The primers for 2.0 kb human PlGF promoter region were 5′-GCG GTAC CCA AAC TCA TAC ACA ATA GAC-3′ (forward primer; italic, KpnI site) and 5′-TTA AGCT TCC GTA GGT AAG GCT GTG GCT-3′ (reverse primer; italic, HindIII site). The amplified DNA fragments were cloned into pGL3 vector (Promega, WI, USA) and the sequences were confirmed by DNA sequence analysis. The pGL3 with mouse PlGF promoter was as previously described [27 (link)].
7
Quantifying KSHV Viral Genome Replication
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To measure viral genome replication, iSLK-BAC16 cells were reactivated for 72 h as described above. The cells were then scraped into the media and the media + cells were digested with proteinase K (80μg/mL) (Promega) in 5x proteinase K digestion buffer (50mM Tris-HCl pH 7.4, 500mM NaCl, 5mM EDTA, 2.5% SDS) overnight at 55°C. The gDNA was isolated using Zymo Quick gDNA Miniprep Kit according to the manufacturer’s instructions. Quantitative PCR (qPCR) was performed on the isolated DNA using iTaq Universal SYBR Green Supermix on a QuantStudio3 Real-Time PCR machine. DNA levels were quantified using relative standard curves with primers specific for KSHV ORF59 promoter and human CPSF6 promoter (S1 Table ). The relative genome numbers were normalized to CPSF6 to account for loading differences and to uninduced samples to account for differences in starting genome copy number.
8
Genome-wide DNA Methylation Profiling
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Genomic DNA from buffy coat samples was isolated using the Quick-gDNA MiniPrep kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocol. Genome-wide methylation analysis was carried out using the Illumina Infinium HumanMethylation450 BeadChip platform at the UCLA Neuroscience Genomics Core in two separate batches. Raw data was summarized into BeadStudio IDAT files for further analysis.
9
Genome-wide DNA Methylation Profiling
10
Genotyping of TGF-β1 and PPARγ2 Polymorphisms
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All genotyping investigations in mothers and newborns were performed on genomic DNA isolated from fresh peripheral blood collected on EDTA, using the Clean-Spin column technology available with the Quick-gDNA MiniPrep Kit (ZymoResearch, Irvine, CA). The TGF-β1 869 T > C gene polymorphism was evaluated by ARMS-PCR (amplification refractory mutation system–polymerase chain reaction) method, as previously described[47 (link)] and the PPARγ2 34 C > G gene polymorphism was investigated by PCR-RFLP (restriction fragment length polymorphism) assay, as previously described by Oh et al.[48 (link)]
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