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5 protocols using ezna tm blood dna midi kit

1

Genotyping Protocol for SNP Analysis

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Peripheral blood (3-5 mL) was collected using tubes coated with ethylenediaminetetraacetic acid (EDTA) and stored at -80°C. Genome DNA was extracted using an EZNA TM Blood DNA Midi Kit (Omega Bio-Tek, Norcross, GA, USA), according to the manufacturer instructions. DNA was stored at -80°C for SNP analysis. Genotyping was carried out on a MassARRAY platform (Sequenom, San Diego, CA, USA). The target fragments were augmented by polymerase chain reaction (PCR). All the products were treated with shrimp alkaline phosphatase. Single nucleotide extension was then carried out using iPLEX enzyme (Sequenom). The samples were spotted onto a 384-well spectroCHIP nanodispenser (Sequenom) and analyzed using the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MassARRAY system in the fully automated mode. Genotypes were automatically identified using SpectroTYPER software (Sequenom).
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2

Genomic DNA Extraction and SNP Genotyping

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Three to five milliliters of peripheral blood was collected in tubes coated with EDTA. Genomic DNA was extracted from the leukocytes in the blood using the EZNA TM Blood DNA Midi Kit (Omega Bio-Tek, Norcross, GA, USA), according to the manufacturer protocol. Primers for PCR and single-base extension were designed by using the Assay Designer software package (Sequenom Inc., San Diego, CA, USA). SNP genotyping was performed by Shanghai Benegene Biotechnology Co., Ltd. (Shanghai, China) using the MassARRAY system (Sequenom) by means of matrix-assisted laser desorption ionization-time of flight mass spectrometry method (MALDI-TOF) according to manufacturer instructions. The completed genotyping reactions were spotted onto a 384-well spectroCHIP (Sequenom) using the MassARRAY Nanodispenser (Sequenom) and determined by MALDI-TOF. Genotype calling was performed in real-time with the MassARRAY RT software version 3.0.0.4 and analyzed using the MassARRAY Typer software version 3.4 (Sequenom).
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3

Genotyping of Blood Leukocyte SNPs

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Genomic DNA was extracted from blood leukocytes using an EZNA TM Blood DNA Midi Kit (Omega Bio-Tek, Norcross, GA, USA), according to the manufacturer instructions. Genotyping for the eight SNPs was performed using the MassARRAY platform (Sequenom, San Diego, CA, USA) by means of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, according to the manufacturer instructions. Primers were designed using the Sequenom software (Table 1), and the extension reaction produced allele-specific products with masses differing by 30 Da, or approximately one single nucleotide. Primer extension and polymerase chain reaction were performed according to the manufacturer instructions using an iPLEX enzyme (Sequenom) and HotStarTaq DNA polymerase (Qiagen, Hilden, Germany). Genotypes were automatically identified by the SpectroTYPER software (Sequenom), and only conservative and moderate calls, as defined by the software, were accepted for this study.
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4

Genomic DNA Extraction and X-Chromosome Sequencing

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Peripheral blood was collected from the enrolled subjects in tubes coated with EDTA. Genomic DNA was extracted from blood leukocytes using the EZNA TM Blood DNA Midi Kit (Omega Bio-Tek, Norcross, GA, USA) according to the manufacturer protocol. All samples were stored at -20°C until use. SSHunter software was used for sequencing the X-chromosome, and Primer 5.0 software (Premier Biosoft, Palo Alto, CA, USA) was used to design primers.Briefly, the 12-µL polymerase chain reaction (PCR) included the following reagents: 50-200 ng genomic DNA, 2X PCR buffer, 15 mM MgCl 2 , 5 µM primers, and 0.5 U Taq polymerase (Tiangen Biotech, Beijing, China). The primer sequences and PCR amplification cycle parameters for the 5lociare listed in Table 1. For allele typing, 6% polyacrylamide gel electrophoresis and silver staining were used, and the alleles were named according to the number of repeats in the sequences based on the recommendations of the International Society of Forensic Genetics.
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5

Genomic DNA Extraction and SNP Genotyping

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Peripheral blood (3-5 mL) was obtained from all patients in tubes coated with EDTA. Genomic DNA was extracted from blood leukocytes using an EZNA TM Blood DNA Midi kit (Omega Bio-Tek, Norcross, GA, USA) according to the manufacturer protocols. Primers for PCR and single-base extension were designed using the Assay Designer software package (Sequenom Inc., San Diego, CA, USA) (Table 1). SNP genotyping was performed using the SNaPshot SNP technology according to the manufacturer protocols. Primary data were analyzed by GeneMapper 4.1 (Applied Biosystems, Foster City, CA, USA). The genotypes were determined based on the nucleotide present at the SNP site, as visualized by one or two differently colored peaks in the chromatograms. For quality control, 5% of the recruited subjects were randomly genotyped twice by researchers in a blind manner, with a reproducibility of 100%.
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