Genomic DNA was extracted from peripheral blood by using a QIAamp DNA Blood Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer's instructions. The primers for SNP genotyping were designed using MassArray Assay Design v4.0 according to the sequence information flanking the SNP, were synthesized by Invitrogen and were validated by MassArray Analyzer Compact. The PCR, removal of free dNTP and sequencing by MassArray Analyzer Compact (Sequenom, San Diego, CA, USA) were performed according to the manufacturer's instructions.
Massarray compact analyzer
Manufactured by Labcorp
Sourced in United States
The MassARRAY Compact Analyzer is a laboratory instrument designed for targeted genetic analysis. It utilizes mass spectrometry technology to accurately detect and quantify specific genetic markers or mutations in samples. The core function of the MassARRAY Compact Analyzer is to provide precise genetic analysis for research and diagnostic applications.
Automatically generated - may contain errors
Lab products found in correlation
Qiaamp dna blood mini kit, by Qiagen (1 mentions)
Pi 103, by Selleck Chemicals (1 mentions)
Bkm120, by Selleck Chemicals (1 mentions)
Byl719, by Selleck Chemicals (1 mentions)
Gdc0032, by Selleck Chemicals (1 mentions)
Bx795, by Selleck Chemicals (1 mentions)
Blasticidine, by Thermo Fisher Scientific (1 mentions)
Everolimus, by Selleck Chemicals (1 mentions)
Sirolimus, by Selleck Chemicals (1 mentions)
Gdc 0941, by Selleck Chemicals (1 mentions)
Azd1208, by Selleck Chemicals (1 mentions)
Pp242, by Selleck Chemicals (1 mentions)
Bx 912, by Selleck Chemicals (1 mentions)
Gdc 0068, by Selleck Chemicals (1 mentions)
Qiaamp dna blood maxi kit, by Qiagen (1 mentions)
Spectrochip, by Labcorp (1 mentions)
Clean resin, by Labcorp (1 mentions)
Human adiponectin elisa kit, by R&D Systems (1 mentions)
7900ht fast real time polymerase chain reaction system, by Thermo Fisher Scientific (1 mentions)
Ge logiq p5 scanner, by GE Healthcare (1 mentions)
17 protocols using massarray compact analyzer
1
Genomic DNA Extraction and SNP Genotyping
2
Cell Line Characterization and Compound Screening
3
Genotyping of FIND SNP rs955333
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The SNP reported by Family Investigation of Nephropathy and Diabetes (FIND), which reaches genome-wide significance, were genotyped. Genotyping was performed by primer extension of multiplex products with detection by matrix-assisted laser desorption ionisation-time of flight mass spectroscopy by a MassARRAY Compact Analyzer (Sequenom, San Diego, CA, USA). Approximately, 1884 individuals and SNP rs955333 were reserved for further analysis after the quality control.
4
Genotyping of GIP and GIPR SNPs
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According to Nakayama et al.,15 (link) six tag single-nucleotide polymorphisms (SNPs) of GIP located between 30 kb upstream and 30 kb downstream of the GIP region were selected based on the HapMap Phase III JPT+CHB database using a threshold of r2⩾0.8. We also selected four tag SNPs for GIPR that were located between 8 kb upstream and 24 kb downstream of the GIPR gene. These SNPs tag 100% of common SNPs with a minor allele frequency of >0.05. All of the SNPs were genotyped with a MassARRAY Compact Analyzer (Sequenom, San Diego, CA, USA). All of the SNPs passed quality control with call rates >95% and concordant rates >99%.
5
Taggin CRP Gene Variants in Han Chinese
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In this study, we selected four tagging SNPs (rs2808629, rs3093077, rs1130864 and rs2808634) that spanned 11 kb in the upstream and 6 kb in the downstream region of CRP, according to HapMap phase III (release 28) Han Chinese database with a threshold of r2 ≥ 0.8. We could tag 95% SNPs (21 out of 22 SNPs) with a minor allele frequency (MAF) > 0.01 within CRP region. All genotyping was done using the primer extension of multiplex products with detecting by matrix-assisted laser desorption ionization-time of flight mass spectroscopy using a MassARRAY Compact Analyzer (Sequenom, San Diego, CA, USA). The genotyping data underwent a series of quality control checks and cleaned data were used in further statistical analysis. The call rates for rs2808629, rs3093077, rs1130864 and rs2808634 were 97.0%, 95.9%, 98.3% and 96.9%, respectively. The concordance rates based on 100 duplicates were over 99% for all these SNPs. Thirty-seven individuals were excluded from the sample call rate checks. The Hardy-Weinberg equilibrium test was performed before the association analysis, and all the four SNPs were in accordance with Hardy-Weinberg equilibrium (P = 0.68 for rs2808629, P = 0.74 for rs3093077, P = 0.34 for rs1130864 and P = 0.47 for rs2808634, respectively).
6
Genotyping Vitamin D Pathway Genes
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DNA was extracted from LH blood pellets with QIAGEN QIAamp DNA Blood maxi kit. The genotyping of DBP and vitamin D-hydroxylase gene variants known to be associated with vitamin D status and of well-described VDR variants was performed at the Vesalius Research Center (Katholieke Universiteit, Leuven, Belgium) by iPLEX technology on a MassARRAY compact analyzer (Sequenom Inc) (21 (link)).
7
MALDI-TOF Mass Spectrometry of Post-PCR Samples
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Example 3
SAP/Post-PCR Reaction: 5 ul Univ PCR was dispensed in a 384 well plate and 2 ul SAP reaction containing 0.6 U SAP (shrimp alkaline phosphatase) were added with incubation at 37° C. for 40 minutes and finally inactivation of the enzyme at 85° C. for 5 minutes. Extension reagents were added in 2 ul amounts containing 0.9 mM acyclic terminators and 1.353 U post-PCR enzyme. The extension oligonucleotide mixture differed in concentration according to its mass: 0.5 uM of low mass: 4000-5870 daltons, 1.0 uM of medium mass: 6000-7350 daltons and 1.5 uM of high mass: 7400-8700 daltons were added in a final volume of 9 ul. The cycling conditions used for post-PCR reaction were 94° C./30 sec and 40 cycles of an 11 temperature cycle (94° C./5 secs and 5 internal cycles of (52° C./5 sec and 80° C./5 sec) and final extension at 72° C./3 minutes.
MALDI-TOF MS: The extension reaction was diluted with 16 ul water and 6 mg CLEAN Resin (SEQUENOM) was added to desalt the reaction. It was rotated for 2 hours at room temperature. 15 nl of the post-PCR reaction were dispensed robotically onto silicon chips preloaded with matrix (SpectroCHIP®, SEQUENOM). Mass spectra were acquired using a Mass ARRAY Compact Analyzer (MALDI-TOF mass spectrometer, SEQUENOM).
8
Genotyping and Serum Adiponectin Measurement
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Cases and controls were mixed for genotyping, and laboratory personnel were unaware of the case or control status. To ensure quality control and evaluate the intrasubject concordance rate, 50 duplicate samples were randomly genotyped twice. Concordance rates for all assays were >99%. Genotyping of each participant was finished by a MassARRAY compact analyzer (Sequenom, San Diego, CA, USA). The oligonucleotide sequences used for genotyping were shown in Table1 .
The process was as follows: (i) deoxyribonucleic acid isolation; (ii) primer design; (iii) polymerase chain reaction; (iv) neutralization of unincorporated deoxyribonucleoside triphosphates (shrimp alkaline phosphatase reaction); (v) extend reaction; (vi) conditioning of iPLEX Gold reaction products (Sequenom Co., Ltd., San Diego, CA, USA); (vii) application to the SpectroCHIP II array (Sequenom Co., Ltd.); (viii) definition of assays and plates; and (ix) spectrum acquisition and analysis.
Human adiponectin serum levels were measured by enzyme-linked immunosorbent assay according to the protocol provided by the manufacturer (human adiponectin ELISA kit; R&D Systems, Abingdon, UK. Standard range: 0.156–10 ng/mL; sensitivity: 0.1 ng/mL; intra-assay precision: <5–10%; interassay precision: <15%; specificity: this assay recognizes recombinant and natural human sdiponectin/Acrp30).
The process was as follows: (i) deoxyribonucleic acid isolation; (ii) primer design; (iii) polymerase chain reaction; (iv) neutralization of unincorporated deoxyribonucleoside triphosphates (shrimp alkaline phosphatase reaction); (v) extend reaction; (vi) conditioning of iPLEX Gold reaction products (Sequenom Co., Ltd., San Diego, CA, USA); (vii) application to the SpectroCHIP II array (Sequenom Co., Ltd.); (viii) definition of assays and plates; and (ix) spectrum acquisition and analysis.
Human adiponectin serum levels were measured by enzyme-linked immunosorbent assay according to the protocol provided by the manufacturer (human adiponectin ELISA kit; R&D Systems, Abingdon, UK. Standard range: 0.156–10 ng/mL; sensitivity: 0.1 ng/mL; intra-assay precision: <5–10%; interassay precision: <15%; specificity: this assay recognizes recombinant and natural human sdiponectin/Acrp30).
9
Genotyping of BMI-associated SNPs
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Genomic DNA was extracted from blood samples collected from each subject. A total of 57 SNPs associated with BMI, waist circumference, and waist-to-hip ratio from previous literature (as shown in Supplementary Table 1 and Supplementary Figure 1 ) were selected to be genotyped using the MassARRAY Compact Analyzer (Sequenom, San Diego, CA, USA). None of the 57 SNPs failed quality control analyses, with call rates >95% and concordant rates >99%. Fifty-three subjects were excluded due to sample call rate <90%. The Hardy-Weinberg equilibrium test was performed prior to the analysis. Among the 57 SNPs, 56 SNPs were in accordance with Hardy-Weinberg equilibrium (P > 0.05), except for rs11118316.
10
Genotyping of Uric Acid-Associated SNPs
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Fifteen SNPs from or near 11 loci (PDZK1 rs12129861, GCKR rs780094, LRP2 rs2544390, SLC2A9 rs11722228, rs16890979, rs3775948 and rs10489070, ABCG2 rs2231142, LRRC16A rs742132, SLC17A1 rs1183201, SLC17A3 rs1165205, rs1333049, SLC22A11 rs17300741, SLC22A12 rs506338, SF1 rs606458) were selected based on the literature and have been reported to be associated with serum uric acid levels [14 (link), 19 (link)]. The SNPs were genotyped using a multiplex primer extension, with detection by matrix-assisted laser desorption/ionisation time-of-flight mass spectroscopy with a MassARRAY Compact Analyzer (Sequenom, San Diego, CA, USA). All 15 SNPs passed the quality control criteria with genotyping call rates greater than 90%. Individuals with more than 10% of the genotypes missing were excluded.
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