Genomic DNA was isolated from N. gonorrhoeae isolates and control strains (WHO F, L, O, G, M, P, N, and K) [38 (link)] using the Quick-DNA™ Miniprep Plus Kit (Zymo Research, CA, USA) as per the manufacturer's instruction. DNA was extracted from patient specimens as follows: swabs were vortexed for 30 s while inside their Eswab® transport tubes, whereafter 200 µL of the suspension was added to a 1.5 mL Eppendorf tube, and the Quick-DNA™ Miniprep Plus Kit (Zymo Research, CA, USA) was used as per the manufacturer's instruction.
Quick dna miniprep plus kit
Manufactured by Zymo Research
Sourced in United States
The Quick-DNA Miniprep Plus Kit is a laboratory product designed for the rapid and efficient isolation of high-quality genomic DNA from a variety of sample types. It utilizes a spin-column format to streamline the DNA extraction process.
Automatically generated - may contain errors
Lab products found in correlation
Qubit 3.0 fluorometer, by Thermo Fisher Scientific (12 mentions)
4d nucleofector, by Lonza (6 mentions)
Nanodrop one, by Thermo Fisher Scientific (6 mentions)
Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (6 mentions)
Ez dna methylation gold kit, by Zymo Research (5 mentions)
Abi 3730xl genetic analyzer, by Thermo Fisher Scientific (5 mentions)
Solution se, by Lonza (4 mentions)
Miseq instrument, by Illumina (4 mentions)
Tapestation 2200, by Agilent Technologies (4 mentions)
Genemapper 5, by Thermo Fisher Scientific (4 mentions)
Quick rna miniprep kit, by Zymo Research (3 mentions)
850 epic arrays, by Illumina (3 mentions)
Karyostat assay, by Thermo Fisher Scientific (3 mentions)
Dna dot blot protocol, by Cell Signaling Technology (3 mentions)
Powerplex 16 system, by Promega (3 mentions)
Nextseq 500, by Illumina (3 mentions)
Purelink genomic dna kit, by Thermo Fisher Scientific (3 mentions)
Steponeplus real time pcr system, by Thermo Fisher Scientific (3 mentions)
S220 focused ultrasonicator, by Covaris (2 mentions)
Cpgenome universal dna modification kit, by Merck Group (2 mentions)
175 protocols using quick dna miniprep plus kit
1
Genomic DNA Isolation from Neisseria gonorrhoeae
2
Telomere Length Quantification Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genomic DNA (gDNA) extraction was conducted using the protocol of the Quick-DNA™ Miniprep Plus Kit (Zymo Research, Irvine, CA, USA). In total, 1 × 106 harvested cells were used for the gDNA extraction. A NanoDrop™ 2000 was used for gDNA quantification and quality assessment. The quantification of the relative telomere length was done according to Vasilishina et al. [62 ] with minor adjustments, whereby 10 ng of gDNA and a GoTaq® 2-Step RT-qPCR System were used. The amplification was done for 40 cycles and conducted using StepOnePlus™ RT-PCR Systems. Single copy gene (SCG), interferon beta 1 (IFNB1) was used for normalization.
3
Rapid Blood DNA Extraction for Research
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA extraction from patients’ and healthy controls’ peripheral blood will be performed using commercially available reagent Quick-DNA Mini-Prep Plus kit (Zymo Research, USA) following manufacturer’s instructions.
4
Assessing Drug Sensitivity in E. coli
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
We first performed a drug sensitivity experiment using E. coli BW25113 and calculated the IC90 for 5-FU and FUDR in nutrient-poor and nutrient-rich media. For nutrient-rich media, we used 100 μM 5-FU and 24 μM FUDR, and for nutrient-poor media we used 2.7 μM 5-FU and 2.3 μM FUDR. We inoculated 15 μl of the glycerol stock of the pooled strain library into 25 ml of the two media types for overnight growth (this high inoculum was used to maintain a high population size and avoid a sampling bottleneck in the thawing stage). In the morning we diluted the culture to OD600 of 1 and again diluted them 1:200 into 7 ml media supplemented with drugs to start the screen. We performed the screens in biological duplicates. We monitored the optical density of cultures throughout the screen. When the cultures reached OD600 of 0.6 we stopped the experiment and immediately extracted DNA (Zymo Quick DNA Miniprep Plus Kit, Cat#D4068).
5
Quantifying Mitochondrial DNA Levels
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Twenty-five (25) mg of heart tissue was added to 95 µL nuclease-free water (NFW), 95 µL solid tissue buffer, and 10 µL proteinase K. The mixture was incubated for 90 minutes, and the tissue was homogenized using a micro pestle. The determination of the mitochondrial DNA (mtDNA) copy number was carried out in a qRT-PCR machine. Total DNA was isolated from cardiac homogenates using the Quick-DNA Miniprep Plus Kit (Zymo Research). The primers were designed to detect cytochrome c oxidase subunit II (COII) for mitochondrial DNA (mtDNA) and β-actin for nuclear DNA (nDNA), according to Santos et al.5 A total of 50 ng of template DNA was added to the qPCR reaction mixture consisting of 10 µL of ThunderbirdTM SYBR qPCR mix. The reactions were done following the manufacturer’s methods. The cycle threshold value (Ct) of COII and β-actin in each sample was used to obtain the ratio of mtDNA to nDNA. The full sequences of the primers are provided in Supplementary Table 3
6
Blood Leukocyte DNA Isolation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Leukocytes were isolated from the blood samples taken into 2 mL EDTA tubes from the patients and control group individuals in the study. DNA isolation was performed from the leukocytes with the Quick-DNA Miniprep Plus Kit (Zymo Research) commercial kit according to the manufacturer’s instructions. DNA samples were stored at -20°C.
7
DNA Extraction and Nanopore Sequencing
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA was extracted using a Zymo Quick-DNA Miniprep Plus kit, (catalog number D4068, Zymo Research, Irvine, CA), according to manufacturer’s instructions. Due to sample timing availability and flow cell upgrade paths, we performed sequencing with two different flow cell types over three flow cells. For each of three pools, approximately 50 individuals were used for extraction, generating 1 μg of DNA which was loaded into the library prep kit. Libraries were prepared using the SQK-LSK110 and SQK-LSK114 ligation sequencing kits for flow cells R9.4.1 and R10.4.1 respectively. Sequencing was carried out for 24 hours per flow cell. Bases were called using the guppy basecaller v6.3.9 with model ‘dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_sup.cfg’.
8
Quantifying HSV-1 Lytic mRNA and DNA
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To assess relative expression of HSV-1 lytic mRNA, total RNA was extracted from approximately 1.0 × 104 neurons using the Quick-RNA Miniprep Kit (Zymo Research) with an on-column DNase I digestion. mRNA was converted to cDNA using the SuperScript IV First-Strand Synthesis system (Invitrogen) using random hexamers for first-strand synthesis and equal amounts of RNA (20–30 ng/reaction). To assess viral DNA load, total DNA was extracted from approximately 1.0 × 104 neurons using the Quick-DNA Miniprep Plus Kit (Zymo Research). qPCR was carried out using Power SYBR Green PCR Master Mix (Applied Biosystems). The relative mRNA or DNA copy number was determined using the Comparative CT (ΔΔCT) method normalized to mRNA or DNA levels in latently infected samples. Viral RNAs were normalized to mouse reference gene GAPDH. All samples were run in duplicate on an Applied Biosystems QuantStudio 6 Flex Real-Time PCR System and the mean fold change compared to the reference gene calculated. Primers used are described in Key Resources Table.
9
Saliva DNA Extraction Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA was extracted from 150 saliva samples using the Quick-DNA Miniprep Plus Kit (Zymo Research; Irvine, California, United States), following the manufacturer’s protocol. The extracted DNA was stored at–20°C until further analysis.
10
Mutation Analysis of Cell Lines
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
DNA was extracted from the cell lines BdEC, T24, and SV-HUC-1 using a ZymoResearch (Irvine, CA, USA) Quick DNA Miniprep Plus kit (D4068). Mutation analysis was performed using the Archer VariantPlex Myeloid Panel (Diagnostica Longwood, Zaragoza, Spain), an NGS panel containing the KDM6A gene. Mutation calling was performed using ArcherDx Analysis (Version 6.2.7) with default settings using the Gen-ERA NGS service.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!