Geneamp 7900 sequence detection system

Manufactured by Thermo Fisher Scientific

Sourced in United States

The GeneAmp 7900 Sequence Detection System is a real-time PCR instrument designed for quantitative gene expression analysis. It utilizes fluorescence-based detection to monitor the amplification of DNA sequences in real-time during the PCR process.

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Lab products found in correlation

Qiaamp dna blood midi kit, by Qiagen (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Superscript 3 reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Oligo dt 12 18, by Thermo Fisher Scientific (1 mentions) Quantitect sybr green pcr kit, by Qiagen (1 mentions) Sybr green, by Thermo Fisher Scientific (1 mentions) Dnase 1, by Thermo Fisher Scientific (1 mentions) Tri reagent, by Molecular Research Center (1 mentions) Taqman reverse transcription rt reagent, by Thermo Fisher Scientific (1 mentions) Comparative threshold cycle ct method, by Thermo Fisher Scientific (1 mentions) Taqman microrna reverse transcription kit, by Thermo Fisher Scientific (1 mentions)

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7900 Sequence Detection System (52 citations) GeneAmp 7900 (6 citations) Sequence Detection Systems (5 citations)

8 protocols using geneamp 7900 sequence detection system

SNP rs6499640 Genotyping Protocol

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Genomic DNA was isolated from peripheral white blood cells using the salt
fractionation method. The SNP rs6499640 was genotyped using the TaqMan Allelic
Discrimination Assay with the GeneAmp 7900 Sequence Detection System (Applied
Biosystems, USA). Genotyping call rates for SNP was > 98%. In order to
validate the accuracy of genotyping, we repeated 70 samples randomly for each
SNP and observed 100% concordance between the results of the two tests.

Gao L., Wu L., Zhang M., Zhao X., Cheng H, & Mi J. (2018). Gender-specific association of the rs6499640 polymorphism in the FTO gene with plasma lipid levels in Chinese children. Genetics and Molecular Biology, 41(2), 397-402.

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Metabolic and Genetic Biomarker Profiling

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The level of fasting plasma glucose (FPG) was measured using the hexokinase method. The levels of lipids were measured using the enzymatic methods for triglycerides (TGs) and total cholesterol (TC) measurements, and the clearance methods for high-density lipoprotein cholesterol (HDL) and low-density lipoprotein cholesterol (LDL) measurements. The measurements were performed using a kit assay (SEKISUI Medical Technology, Tokyo, Japan) and an automatic biochemical analyser (Hitachi 7060). The levels of adipocytokines (leptin, adiponectin and resistin) were measured by ELISA techniques.19 (link)
Genomic DNA was isolated from peripheral white blood cells using the salt fractionation method. Genotyping of rs3748024 was conducted using the TaqMan Allelic Discrimination Assay with the GeneAmp 7900 Sequence Detection System (Applied Biosystems, Foster City, CA, USA). The genotyping call rate for the SNP was 98.3%. We repeated 70 samples randomly for the SNP to validate the accuracy of the genotyping and observed 100% concordance between the results of the two tests. We also sent 30 samples to direct sequencing and observed 100% concordance between the two genotyping methods.

Wu L., Gao L., Zhao X., Zhang M., Wu J, & Mi J. (2017). A new risk locus in CHCHD5 for hypertension and obesity in a Chinese child population: a cohort study. BMJ Open, 7(9), e016241.

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Genetic Risk Factors for CAD in Chinese

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We selected only SNPs in CAD-related genes with minor allele frequencies>0.05 in Chinese in the HapMap database. We used the SNPs effect size in the references, minor allele frequenies of Chinese (based on HapMap database) and sample size of this study to calculate the power for detecting positive association. Exclude the SNPs which the power less than 0.20, we chose nine SNPs (rs10953541, rs1122608, rs12190287, rs12413409, rs1412444, rs1746048, rs3798220, rs4977574, rs579459) that have been shown to significantly associate with CAD but not yet tested in the Chinese population.
Genomic DNAs were extracted from leukocytes using QIAamp DNA Blood Midi Kit (QIAGEN, Germany) according to the manufacture's protocol. SNPs were genotyped by TaqMan Allelic Discrimination Assays with the GeneAmp 7900 Sequence Detection System (Applied Biosystems, Foster City, CA). TaqMan probes were used for genotyping rs10953541 (C_2618842_20), rs1122608 (C_27208850_10), rs12190287 (C_32243431_10), rs12413409 (C_2852843_10), rs1412444 (C_8870364_10), rs1746048 (C_2086883_10), rs3798220 (C_25930271_10), rs4977574 (C_1754681_10), rs579459 (C_26744819_10). Genotyping call rates for all SNPs were greater than 98% (Table S1).

Wang Y., Wang L., Liu X., Zhang Y., Yu L., Zhang F., Liu L., Cai J., Yang X, & Wang X. (2014). Genetic Variants Associated with Myocardial Infarction and the Risk Factors in Chinese Population. PLoS ONE, 9(1), e86332.

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Genotyping of Adipocytokine-Related SNPs

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The levels of adipocytokines were measured by ELISA techniques [20 (link)]. Genomic DNA was isolated from peripheral white blood cells using the salt fractionation method. Genotyping of rs17782313 and rs6265 was conducted using the TaqMan Allelic Discrimination Assay with the GeneAmp 7900 Sequence Detection System (Applied Biosystems, Foster City, CA, USA) and with the TaqMan probes (C__32667060_10 and C__11592758_10). The genotyping call rates for both SNPs were greater than 98%. We repeated 70 samples randomly for each SNP to validate the accuracy of genotyping and observed 100% concordance between the results of the two tests. We also sent 30 samples to direct sequencing and observed 100% concordance between two genotyping methods.

Wu L., Gao L., Zhao X., Zhang M., Wu J, & Mi J. (2017). Associations of Two Obesity-Related Single-Nucleotide Polymorphisms with Adiponectin in Chinese Children. International Journal of Endocrinology, 2017, 6437542.

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RNA Isolation, cDNA Synthesis, and qRT-PCR

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Example 7

RNA was isolated using RNeasy mini kits (Qiagen, Valencia, Calif.) according to the manufacturer's instructions. For cDNA synthesis, 500 ng total RNA was transcribed with cDNA transcription reagents using SuperScriptIII reverse transcriptase and oligo(dT)12-18 (InVitrogen, Inc.), according to the manufacturer's instructions. Gene expression was measured in real-time with the GeneAmp 7900 Sequence Detection System (Applied Biosystems) using primers and QuantiTect SYBR Green PCR Kit purchased from Qiagen. The expression level of a gene in a given sample was represented as 2^−ΔΔCtwhere ΔΔCT=[ΔCT_{(experimental)}]−[ΔCT_(medium)] and ΔCT=[CT_{(experimental)}]−[CT_{(housekeeping)}]. Data is presented normalized to the glyceraldehyde phosphate dehydrogenase (GADP).

US09977021B2. CD127 expression inversely correlates with FoxP3 and suppressive function of CD4+ tregs (2018-05-22). The Regents of the University of California [US]. Inventors: Jeffrey A. Bluestone [US], Weihong Liu [US], Amy Putnam [US].

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Quantitative Analysis of mRNA Levels

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Animal tissues were frozen in liquid nitrogen at the time of necropsy and stored at -80°C. RNA was extracted from tissue as described previously^{56 (link)} using Tri-Reagent (Molecular Research Center) according to the instructions of the manufacturer. All RNA was treated with DNAseI (Ambion) to remove genomic DNA contamination. For a quantitative analysis of mRNA levels, 1μg of total RNA from each sample was reverse transcribed in a 50-μl volume (TaqMan reverse transcription [RT] reagent; Applied Biosystems), and 4 μl of cDNA was used for each real-time reaction. RT-PCR was performed using the primers listed in Table S2, SYBR green (Applied Biosystems) and GeneAmp 7900 sequence detection system. Data was analyzed by using the comparative threshold cycle (C_T) method (Applied Biosystems). For macaques, target gene transcription for each sample was normalized to the respective levels of ACTB mRNA and represented as fold change over gene expression in mock-infected, adjacent loop. For mice, target gene transcription for each sample was normalized to the respective levels of Gapdh mRNA and represented as fold change over gene expression in control animals.

Mooney J.P., Butler B.P., Lokken K.L., Xavier M.N., Chau J.Y., Schaltenberg N., Dandekar S., George M.D., Santos R.L., Luckhart S, & Tsolis R.M. (2014). The mucosal inflammatory response to non-typhoidal Salmonella in the intestine is blunted by IL-10 during concurrent malaria parasite infection. Mucosal immunology, 7(6), 1302-1311.

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Genetic and Biochemical Analysis of Lipids and Adipocytokines

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Total cholesterol (TC), low-density lipoprotein cholesterol (LDL), high-density lipoprotein cholesterol (HDL), triglycerides (TG), were analyzed by an automatic biochemical analyzer (Hitachi 7060) using a kit assay (SEKISUI medical technology Ltd., Tokyo, Japan). The levels of adipocytokines were measured by ELISA techniques [15 (link)]. Genomic DNA was isolated from peripheral white blood cells using the salt fractionation method. Genotyping of rs11191548 was conducted using the TaqMan Allelic Discrimination Assay with the GeneAmp 7900 Sequence Detection System (Applied Biosystems, Foster City, CA, USA), with the TaqMan probes (C_31979323_10). The genotyping call rate for the SNP was 97.9%. We sent 30 samples to direct sequencing and observed 100% concordance between two genotyping methods. We also repeated 70 samples randomly for the SNP to validate the accuracy of genotyping and observed 100% concordance between the results of the two tests.

Wu L., Gao L., Zhao X., Zhang M., Wu J, & Mi J. (2018). Associations of the hypertension-related single nucleotide polymorphism rs11191548 with high-density lipoprotein cholesterol and leptin in Chinese children. BMC Medical Genetics, 19, 9.

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Quantification of miR-125b Expression

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To detect miR-125b, cDNA was synthesized using a TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems). Relative miR-125b expression was determined on a Gene Amp 7900^® Sequence Detection System (Applied Biosystems). The expression levels of miR-125b in each sample were normalized to the corresponding level of snU6 or geometric mean of snU6, miR-16, and miR-122. The relative expression of miR-125b obtained from the serum and liver tissues was quantified according to the expression 2^-ΔCt using a logarithmic transformation. The expression levels of miR-125b-1 and miR-125b-2 were determined using TaqMan^® Gene Expression Assays. The expression ratios were calculated as the normalized CT difference between the control and sample and were adjusted for amplification efficiency relative to the expression level of the housekeeping gene, snU6.

Dai C.Y., Tsai Y.S., Chou W.W., Liu T., Huang C.F., Wang S.C., Tsai P.C., Yeh M.L., Hsieh M.Y., Huang C.I., Vanson Liu S.Y., Huang J.F., Chuang W.L, & Yu M.L. (2018). The IL-6/STAT3 pathway upregulates microRNA-125b expression in hepatitis C virus infection. Oncotarget, 9(13), 11291-11302.

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