Blood samples were collected in EDTA tubes and stored at −80 °C after centrifugation. DNA extraction carried out using the standard phenol–chloroform extraction method. DNA quantity was evaluated by spectrometry (DU530 UV/VIS spectrophotometer, Beckman Instruments, Fullerton, CA). Four tag SNPs (rs975263, rs1990172, rs3735615 and rs4721888) were selected for our study; these SNPs were with minor allele frequencies >5% in the HapMap Chinese Han Beijing (CHB) population (http://www.hapmap.org ). All selected polymorphisms are located in coding regions with the exception of rs1990172, which is located in an intron (Figure 1 ). Sequenom MassARRAY Assay Design 3.0 Software (Sequenom, Inc, San Diego, CA) was used to design a Multiplexed SNP MassEXTEND assay. We genotype the 4 polymorphisms in all subjects using a Sequenom MassARRAY RS1000 (Sequenom, Inc). Primers of PCR which were used for each SNP in our study are listed in Table 2 . Sequenom Typer 3.0 Software (Sequenom, Inc) was used for data analyses.
Sequenom typer 3
Manufactured by Labcorp
The Sequenom Typer 3.0 Software is a tool designed for the processing and analysis of genetic sequencing data. It provides a platform for the management and interpretation of sequencing results, enabling users to extract meaningful insights from genetic information.
Automatically generated - may contain errors
Lab products found in correlation
Sequenom massarray assay design 3, by Labcorp (3 mentions)
Massarray rs1000, by Labcorp (3 mentions)
Du530 uv vis spectrophotometer, by Beckman Coulter (1 mentions)
Sequenom massarray rs1000, by Labcorp (1 mentions)
Nanodrop 2000, by Thermo Fisher Scientific (1 mentions)
Nanodrop, by Thermo Fisher Scientific (1 mentions)
4 protocols using sequenom typer 3
1
Genotyping of SNPs in Chinese Han Population
2
Genetic Associations of ZNF208 in Esophageal Cancer
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Few studies have investigatedinvestigate the associations between SNPs in the ZNF208 and esophageal cancer. We searched Pubmed and the Hapmap database for ZNF208 SNPs with a MAF > 0.05 in the Chinese Han population. Five SNPs (rs2188972, rs2188971, rs8103163, rs7248488, and rs8105767) were selected for our study. Genomic DNA was extracted from the whole blood samples using the GoldMag-Mini Purification Kit (GoldMag Co. Ltd. Xian, China) according to the manufacturer's instructions. DNA concentrations were measured using a NanoDrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA). SNPs were genotyped using the Sequenom MassARRAY RS1000 and the manufacturer's protocol [30 (link)]. The Sequenom MassARRAY Assay Design 3.0 software was used to design a multiplexed SNP MassEXTEND assay [31 ]. The Sequenom Typer 3.0 Software (Sequenom, Inc) was used for data management and analyses [30 (link), 31 ].
3
POLK SNP Genotyping Protocol
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Blood samples from patients and healthy controls were collected in EDTA-containing tubes. DNA was extracted from peripheral blood samples following standard phenol–chloroform extraction procedure. The extracted DNA was quantitated spectrophotometrically and stored at −80 °C until further use. Three tag SNPs (rs3213801, rs10077427, and rs5744533) were selected for our study; according to the Chinese population data available through HapMap project (http://www.hapmap.org), these SNPs represented the majority of known common variants of POLK. Sequenom MassARRAY Assay Design 3.0 Software (Sequenom, Inc., San Diego, CA) was used to design a Multiplexed SNP MassEXTEND assay. SNP genotyping was performed with a Sequenom MassARRAY RS1000 (Sequenom, Inc.) following the standard protocol recommended by the manufacturer. The corresponding primers used for each SNP in our study are listed in Table 1 . Data analyses were performed using Sequenom Typer 3.0 Software (Sequenom, Inc.).
4
DNA Isolation and SNP Genotyping Protocol
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Whole blood samples were collected in tubes containing ethylene diamine tetraacetic acid. After centrifugation, the samples were stored at −80°C until further analyses. DNA was isolated from the peripheral blood samples using the GoldMag DNA Purification Kit (GoldMag Co. Ltd, Xi’an City, China), and the DNA concentration was measured using an ultraviolet spectrophotometer (Nanodrop, Thermo Scientific, Waltham, MA). Two single nucleotide polymorphisms (SNPs), rs1055901 (CC: wild-type genotype, TC: heterozygous mutant genotype, and TT: homozygous mutant genotype) and rs1055902 (TT: wild-type genotype, CT: heterozygous mutant genotype, and CC: homozygous mutant genotype), that constitute the majority of the known variations in megsin, according to t the Chinese population data found in HapMap (http://www.hapmap.org ), were selected for our study. Sequenom MassARRAY Assay Design 3.0 software (Sequenom Inc, San Diego, CA) was used to design the multiplexed SNP MassEXTEND assay. SNP genotyping was performed using Sequenom MassARRAY RS1000 according to the standard protocol recommended by the manufacturer. The primers used for each SNP are shown in Table 1 . Sequenom Typer 3.0 software (Sequenom Inc) was used for data analyses.
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