Genomic DNA of K. pneumoniae isolates was extracted using the Tissue Genomic DNA Extraction Mini Kit (FAVORGEN Biotech Corporation, Taiwan). Subsequently, specific genes for capsular serotypes K1 and K2 and virulence genes including rmpA, rmpA2, iutA, iucA, iroB, kfu, allS, entB, ybtS, clbA, as well as the β-lactamase genes such as blaTEM, blaSHV, blaCTX-M, blaKPC, blaNDM, and blaOXA-48 were identified by PCR with the specific primers (Table 1 http://www.ncbi.nlm.nih.gov/blast/ ).
Tissue genomic dna extraction mini kit
Manufactured by Favorgen Biotech
Sourced in United States
The Tissue Genomic DNA Extraction Mini Kit is a laboratory equipment designed for the extraction and purification of DNA from various tissue samples. It utilizes a simple and efficient protocol to isolate high-quality genomic DNA suitable for downstream applications such as PCR, sequencing, and analysis.
Automatically generated - may contain errors
Lab products found in correlation
Nanodrop 2000, by Thermo Fisher Scientific (2 mentions)
Qiaamp dna stool mini kit, by Qiagen (2 mentions)
Qiaamp dna blood maxi kit, by Qiagen (2 mentions)
Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions)
Nanodrop 1000, by Thermo Fisher Scientific (2 mentions)
Ez dna methylation gold kit, by Zymo Research (2 mentions)
Peqlab thermocycler, by Avantor (1 mentions)
Kapa sybr fast, by Merck Group (1 mentions)
Betaine, by Merck Group (1 mentions)
Sybr safe dna gel stain, by Thermo Fisher Scientific (1 mentions)
Bst dna polymerase large fragment, by New England Biolabs (1 mentions)
Dntp solution mix, by Promega (1 mentions)
Magnesium sulfate, by New England Biolabs (1 mentions)
Whatman, by Cytiva (1 mentions)
Absolute ethanol, by Merck Group (1 mentions)
Revertaid reverse transcriptase, by Thermo Fisher Scientific (1 mentions)
Nanodrop 2000c spectrophotometer, by Thermo Fisher Scientific (1 mentions)
14 protocols using tissue genomic dna extraction mini kit
1
Genotypic Characterization of K. pneumoniae
2
Genomic DNA Extraction and PCR Amplification
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Purification of DNA was accomplished using the Tissue Genomic DNA Extraction Mini Kit (FavorPrep, FavorGen, Taiwan) following the manufacturer’s instructions. All PCRs were performed in a total volume of 25 μl containing 12.5 μl Super PCR Mastermix 2X (Taq DNA polymerase, dNTP, MgCl2), 1 μl of each primer (10 μM), 1 μl template DNA (100 ng), and 9.5 μl nuclease-free water. PCR runs were carried out on a peQlab Thermocycler (peQlab, UK). The conditions were as follows: initial denaturation at 94 °C for 5 min, 30 cycles at 94 °C for 1 min with annealing temperature at 72 °C for 1 min in between, followed by a final extension at 72 °C for 5 min. Amplified DNA was visualized using electrophoresis in 1% agarose gel in 1× Tris-EDTA buffer.
3
Isothermal DNA Amplification on dPADs
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The reagents and enzyme included Millipore Milli Q water system (R ≥ 18 MΩ cm), magnesium sulfate (New England Biolabs, Ipswich, MA, USA), 1× Thermopol buffer (New England Biolabs), Betaine (Sigma-Aldrich, St. Louis, MO, USA), SYBR™ Safe DNA Gel Stain (Thermo Fisher Scientific, Waltham, MA, USA), dNTP mix solution (Promega Corporation, Madison, WI, USA), Bst DNA Polymerase Large Fragment (New England Biolabs) and KAPA SYBR® FAST (Sigma-Aldrich). The chemical solutions were prepared and made according to Saengsawang et al.38 (link). The tissue Genomic DNA Extraction Mini Kit was purchased from Favorgen® Biotech Corp. (Ping Tung, Taiwan). The dPADs were fabricated from Whatman No. 1 (Vernon Hills, IL, USA), according to Saengsawang et al.38 (link).
4
Fecal DNA Extraction and Quantification
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Genomic DNA of fecal specimens and standard strains were extracted using Qia amp DNA stool mini kit (Qiagen) and the tissue genomic DNA extraction mini kit (Favorgen Biotech Corp), According to the manufacturer's instructions, respectively. Integrity size of DNA were checked by 0.1% agarose gel electrophoresis. DNA concentrations were determined with the Nano Drop 2000 (Thermo. Scientific) and stored at -20°C prior to amplification steps.
5
Pathogen Detection in NPS Samples
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NPS samples were used to extract DNA using Tissue Genomic DNA extraction mini kit (Favorgen Biotech Corp., Taiwan), according to manufacturer’s protocol. The DNA preparation was stored at
−20°C until used for PCR or nested PCR analysis. The detection of three pathogens, M. haemolytica, H. somni and P. multocida, were
performed by PCR as previously described [3 (link), 4 (link), 43 (link)]. M.
bovis detection was performed by nested PCR [35 (link)]. Four samples containing target template bacterial DNA from previous studies in our
laboratory were used as positive controls and distilled water was used as a negative control. The positive controls were verified and compared with the database using BLAST program. After
PCR amplification, each PCR product was electrophoresed by 1.5% agarose gel at 100 V to identify the size of products.
−20°C until used for PCR or nested PCR analysis. The detection of three pathogens, M. haemolytica, H. somni and P. multocida, were
performed by PCR as previously described [3 (link), 4 (link), 43 (link)]. M.
bovis detection was performed by nested PCR [35 (link)]. Four samples containing target template bacterial DNA from previous studies in our
laboratory were used as positive controls and distilled water was used as a negative control. The positive controls were verified and compared with the database using BLAST program. After
PCR amplification, each PCR product was electrophoresed by 1.5% agarose gel at 100 V to identify the size of products.
6
Fecal DNA Extraction and Quantification
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Using Qia amp DNA stool mini kit (Qiagen) and the tissue genomic DNA extraction mini kit (Favorgen Biotech Corp), genomic DNA of fecal specimens and standard strains were extracted. DNA concentrations were determined with the Nano Drop 2000 (Thermo. Scientific) and stored at -20°C prior to amplification steps.
7
Milk DNA Extraction for T. gondii
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The extraction of DNA from milk was carried out by using a DNA isolation kit (Favorgen Tissue Genomic DNA Extraction Mini kit, USA). The extracted DNA was amplified by using primers of B1 gene for T. gondii following the protocol of Sadek et al. (2015) (link). The reaction conditions consisted of one cycle of 95ºC for 5 minutes followed by 40 cycles of 94ºC for 30 seconds, 60ºC for 30 seconds, 72ºC for 1 minute, and final extension at 72ºC for 10 minutes, and then the amplified DNA were electrophoresed on 2% agarose gel. The amplified DNA 115 bp bands were visualized under UV-trans illuminator and compared with a 50 bp DNA ladder marker (thermoisher scientific, USA).
8
Genomic DNA Extraction from Tissue and Blood
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Tumor DNA extraction was performed with Tissue Genomic DNA Extraction Mini Kit (FAVORGEN), according to the manufacturer’s instructions. Blood DNA was extracted with the QIAamp DNA Blood Maxi kit (Qiagen) following the manufacturer’s instructions. Genomic DNA was quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).
9
HPV Genotyping from Cervical Samples
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DNA was extracted from cervical specimens using the Tissue Genomic DNA Extraction Mini Kit (Favorgen Biotech Corp., Ping-Tung, Taiwan) at The University of Tokyo. HPV genotyping was performed at the National Institute of Infectious Diseases using the PGMY-CHUV assay method as described previously [21 (link)]. Briefly, standard PCR was conducted using the PGMY09/11 L1 consensus primer set and human leukocyte antigen-DQ (HLADQ) primer sets. Subsequently, reverse blotting hybridization was performed. Heat-denatured PCR amplicons were hybridized to probes specific for 31 HPV genotypes and HLA-DQ references [22 (link)].
10
DNA Extraction from Chicken Larvae
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DNA was extracted from each larva recovered from the tissues of chickens using the Tissue Genomic DNA Extraction Mini Kit (Favorgen Biotech, Ping-Tung, Taiwan) according to the manufacturer’s instructions. Briefly, 25 mg of the digested sample was transferred to a 1.5 mL Eppendorf tube, suspended in 200 μL lysis buffer (FATG1 Buffer) and 20 μL of Proteinase K. The solution was mixed in a vortex and incubated for up to 3 hr. at 60 °C to lyse the sample. Then, 200 μL FATG2 buffer was added to the sample, mixed thoroughly by pulse-vortexing, and incubated at 70 °C for 10 minutes. The solution was combined with 200 μL of absolute ethanol (Merck, Germany) and it was mixed thoroughly. The mixture was transferred to the FATG Mini Column (supported by the kit) and centrifuged at full speed (~ 18,000 g) for 1 min, then discarded flow-through. After an additional washing with 750 μL of wash buffer, the samples were treated with 100 μL of elution buffer for 3 min at room temperature and centrifuged at full speed for 2 min to elute DNA. Finally, NanoDrop measured the purified DNA concentration (BECO, Germany).
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