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4 protocols using scrfi

1

Rapid LAMP Assay for Salmonella Detection

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Bst DNA polymerase (Large Fragment) was purchased from Vazyme Biotech Co., Ltd. (Nanjing, China). Nt.BstNBI, ScrFI, DraI, and agarose were obtained from New England Biolabs (Ipswich, MA, USA). Syto 9 was achieved from Thermo Fisher (Waltham, MA, USA). 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid (HEPES), hemin, dNTP mixture, and ABTS were all supplied by Sangon Biotech (Shanghai, China) Co., Ltd. LB agar and LB broth were offered by Beijing Land Bridge Technology Co., Ltd. (Beijing, China) 30% H2O2 was bought from Sigma-Aldrich, Inc. (Burlington, MA, USA).
The gene of invasion protein A (invA) was selected as the reference gene for amplification (GenBank accession no. NC_003197). Conventional LAMP primers were synthesized according to the previous report [32 (link)]. Inner primers incorporated with the recognition site (GAGTC) of nicking endonuclease, Nt.BstNBI, are termed as Nick-BIP and Nick-FIP. All the sequences were evaluated with IDT Oligo Analyzer 3.1 (Integrated DNA Technologies, Coralville, IA, USA). The oligonucleotides were synthesized by Sangon Biotech (Shanghai, China) Co., Ltd. Sequences used in this work are listed in Table S1, and the corresponding template sequence is displayed in Figure S1.
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2

Genotyping of IL-31 Gene Polymorphism

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Genomic DNA was extracted from 200 μl EDTA-anticoagulated peripheral blood sample with a DNA isolation kit (BioTeke, Peking, China) as the manufacturer's direction. DNA was stably stored at −20°C until assayed. Genotyping of the IL-31 gene polymorphism was conducted by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). We designed the PCR primers with software Primer 3 (http://bioinfo.ut.ee/primer3‐0.4.0/primer3/) [27 (link)] as shown in Table 1. The 10 μl PCR reaction system was consisted of 1.0 μl DNA and 5 μl 2× Power Taq PCR Master Mix (BioTeke, Peking, China), forward and reverse primer 0.1 μl, respectively, and reserved volume was made up to 10 μl by sterilized water. The PCR condition was designed as 95°C for 4 min firstly, then 33 cycles at 95°C for 30 s, 60°C for 30 s, and 72°C for 30 s, and finally, 72°C for 10 min. Furthermore, the PCR products were digested in 37°C stable incubation by distinguished restriction enzyme MboII (New England Biolabs, Peking, China) for 30 minutes of rs4758680 and ScrFI (New England Biolabs, Peking, China) for 2 hours of rs7977932 as shown in Table 1, separately. Ultimately, the results were visually analyzed by 6% polyacrylamide gels in silver staining. To verify the genotyping results, DNA sequencing was performed in about 20% PCR-amplified DNA samples randomly.
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CCND1 G870A Genotyping by PCR-RFLP

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Genomic DNA was extracted from peripheral blood lymphocytes using a commercially available kit (Promega, Madison, WI, USA) according to manufacturer instructions. DNA samples were stored at -80°C until genotyped. CCND1 G870A genotyping was performed using the polymerase chain reaction (PCR). Primers for amplification of CCND1 were as follows: 5'-GCA GTG CAA GGC CTG AAC CT -3' (sense) and 5'-GGG ACA TCA CCC TCA CTT AC -3' (antisense). PCR was performed in 30 μL volumes containing 1 U Taq polymerase, 5 ng genomic DNA, 10 nM of each primer, and 2.5 μM dNTPs. Thermocycling was carried out at 94°C for 5 min followed by 35 cycles at 94°C for 60 s, 60°C for 60 s, and 72°C for 1 min, with a final incubation at 72°C for 7 min. After confirmation of the 167-bp PCR fragment by 1.5% agarose gel electrophoresis, each PCR product was digested overnight with 5 U ScrFI at 37°C (New England Biolabs Inc., Beverly, MA, USA) and separated by 3.0% agarose gel electrophoresis. The 167-bp PCR fragment was digested into 146-and 22-bp fragments when the ScrFI site was present (Simpson et al., 2001) . The genotype was designated as G or A when the ScrFI restriction site was present or absent, respectively.
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Genotyping Polymorphism by PCR-RFLP

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DNA was extracted from peripheral blood lymphocytes using DNA Blood Mini Kits (A&A Biotechnology, Gdynia, Poland). Genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). PCR was carried out in a volume of 10 µl. The reaction mixture consisted of 100 ng of genomic DNA, 0.5 µmol of each primer and 3 U of Taq polymerase. The PCR cycling conditions consisted of an initial denaturation step of 94°C for 10 minutes, followed by 34 cycles of 94°C for 1 minute, 56°C for 45 s, 72°C for 45 s and final extension of 72°C for 10 minutes.
A 10 µl amount of specifically positive PCR products was digested overnight with 1 µl of ScrFI (New England Bio Labs, Beverly, MA) at 37°C, and the digested DNA fragments were resolved on 3% agarose gel. The randomly selected DNA samples amplified by PCR for each genotype were cross-checked by DNA sequencing, and the results were found to be 100% concordant [27] . The primers, length of PCR products and restriction enzymes are summarized in Table I. Genotypes were designated as follows: 99 bp and 201 bp for C/C; 99, 201 and 300 bp for C/G; and 300 bp for G/G. Figure 1 presents a representative electropherogram obtained after digestion of PCR products.
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