Abi prism 7900 sequence detection system instrument

Manufactured by Thermo Fisher Scientific

Sourced in United States

The ABI PRISM 7900 Sequence Detection System is a real-time PCR instrument used for gene expression analysis, genotyping, and other quantitative PCR applications. It features a 96-well sample block, a sensitive optical system, and specialized software for data analysis and results interpretation.

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Lab products found in correlation

Wizard kit, by Promega (1 mentions) Sds software version 2, by Thermo Fisher Scientific (1 mentions) Nanodrop nd 1000, by Thermo Fisher Scientific (1 mentions) Taqman genotyping assay, by Thermo Fisher Scientific (1 mentions) Vic labeled taqman assays, by Thermo Fisher Scientific (1 mentions) Superscript 3 reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Sds 2, by Thermo Fisher Scientific (1 mentions) Tiangen dna isolation kit, by Tiangen Biotech (1 mentions) Taqman snp genotyping assay, by Thermo Fisher Scientific (1 mentions)

3 protocols using abi prism 7900 sequence detection system instrument

Genotyping of COMT and BDNF Polymorphisms

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Peripheral blood samples were collected from patients in 5 ml EDTA tubes. Genomic DNA was extracted from peripheral blood as recommended by the manufacturer (Wizard kit, Promega). After quality assessment and quantification using NanoDrop ND-1000 (Thermo Scientific, USA), 10 ng of DNA samples were genotyped in 5 μl TaqMan genotyping assay as recommended by the manufacturer (Applied Biosystems, Foster City, CA). Primers and probes for SNPs rs4680 in COMT gene and rs6265 in BDNF gene were purchased from Applied Biosystems (Applied Biosystems, Foster City, CA). The assays were run on an ABI PRISM 7900 Sequence Detection System instrument (Applied Biosystems, Foster City, CA). The genotyping results were analyzed using the SDS software version 2.3 (Applied Biosystems). For quality control, 10% were repeated for the genotyping assay, and the results were 100% concordant.

Huey E.D., Fremont R., Manoochehri M., Gazes Y., Lee S., Cosentino S., Tierney M., Wassermann E.M., Momeni P, & Grafman J. (2020). Effect of functional BDNF and COMT polymorphisms on symptoms and regional brain volume in Frontotemporal Dementia and Corticobasal Syndrome. The Journal of neuropsychiatry and clinical neurosciences, 32(4), 362-369.

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Quantitative Real-Time PCR in Mice

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Real-time PCR was used to assess specific mRNA levels in mouse kidney and lung. Organs were dissected from 1- and 4-wk old C57BL/6 mice (n = 5 animals per time point). Total RNA (100–200 ng) was reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen). Quantitative real-time PCR was performed for 18S, Aurkb, Ccnd2, Sox11, Rrm2, and Zwilch using commercially available FAM or VIC-labeled Taqman assays (Applied Biosystems, Foster City, CA). Reactions were performed in triplicate on cDNA derived from each animal using the ABI prism 7900 Sequence Detection System instrument (Applied Biosystems). The relative quantity of each mRNA was calculated using the formula: Relative Expression = 2^–ΔCt×10⁶, where Ct represents the threshold cycle and ΔCt = (Ct of gene of interest)–(Ct of 18S rRNA). Values were multiplied by 10⁶ for convenience of comparison.

Lui J.C., Chen W., Cheung C.S, & Baron J. (2014). Broad Shifts in Gene Expression during Early Postnatal Life Are Associated with Shifts in Histone Methylation Patterns. PLoS ONE, 9(1), e86957.

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Genotyping Nicotinic Receptor SNPs

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A total of 5 SNPs within CHRNA3 (rs1317286), CHRNA4 (rs1044396), CHRNA7 (rs6494212), and CHRNA5 (rs16969968, rs684513) were selected based on the following criteria: 1) SNPs are capable of tagging more SNPs based on the linkage disequilibrium (LD) pattern of the respective genes according to the data from the HapMap CHB dataset (http://hapmap.ncbi.nlm.nih.gov/) and 1,000 Genomes (http://www.broadinstitute.org/mpg/snap/) and 2) all eligible SNPs should have a minor allele frequency (MAF) >5% according to the HapMap CHB and dbSNP datasets (http://www.ncbi.nlm.nih.gov/SNP/).
Genomic DNA was isolated using a Tiangen DNA isolation kit (Tiangen Biotech, Beijing, China). Genotyping of the SNPs was carried out using the TaqMan SNP Genotyping Assay (Applied Biosystems, Foster City, CA, USA) on ABI PRISM7900 sequence detection system instrument (Applied Biosystems) and SDS 2.0 software (Applied Biosystems). For quality control, all genotypes were determined without knowledge of case or control status in the genotyping process. 5% of the samples were repeated for genotyping and the corresponding results were 100% concordant.

Li Y.Y., Geng R.J., Yu S.Y., Li G.J., Wang Z.Y, & Li H.F. (2021). Association Study of Polymorphisms in Neuronal Nicotinic Acetylcholine Receptor Subunit Genes With Schizophrenia in the Han Chinese Population. Psychiatry Investigation, 18(10), 943-948.

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