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Taqman copy number reference assay human rnasep

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The TaqMan Copy number Reference Assay human RNaseP is a qPCR-based assay designed to quantify the copy number of the human RNase P gene. It provides a reliable reference for copy number variation analysis.

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Lab products found in correlation

Taqman copy number assay, by Thermo Fisher Scientific (1 mentions) Taqman probe based technology, by Thermo Fisher Scientific (1 mentions) Steponeplus real time pcr system, by Thermo Fisher Scientific (1 mentions) Taqpath proamp master mixes, by Thermo Fisher Scientific (1 mentions)

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TaqMan assays (1810 citations) RNaseP (49 citations) RNAseP assay (13 citations) Human TaqMan® Copy Number Reference Assay (2 citations) RNaseP reference assay (2 citations) Human RNaseP (2 citations)

3 protocols using taqman copy number reference assay human rnasep

1

Quantification of Gene Copy Number Variations

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PIK3CA, EGFR, ESR1 and CCND1 gene copy number variations (CNVs) were analyzed by Real-Time PCR, using TaqMan probe-based technology (Applied Biosystems, Foster City California, USA). The RNaseP as housekeeping gene and a normal male breast tissue sample as calibrator were used. TaqMan Copy number Assays (Hs02708380_cn for PIK3CA, Hs00756893_cn for EGFR, Hs02577150_cn for ESR1 and Hs01818912_cn for CCND1) and TaqMan Copy number Reference Assay human RNaseP, containing primers and probe mix for target and housekeeping genes respectively, were used (Applied Biosystems, Foster City California, USA). The analysis of relative gene expression data was performed, using the 2−ΔΔCt method. The fold change in studied gene copy number, normalized to endogenous control, was calculated using RQ=2−ΔΔCt [62 (link)–63 (link)]. Values of RQ ≥2 were considered amplified and values of RQ <0.5 were considered deleted.
Rizzolo P., Navazio A.S., Silvestri V., Valentini V., Zelli V., Zanna I., Masala G., Bianchi S., Scarnò M., Tommasi S., Palli D, & Ottini L. (2016). Somatic alterations of targetable oncogenes are frequently observed in BRCA1/2 mutation negative male breast cancers. Oncotarget, 7(45), 74097-74106.
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2

Quantifying YTHDF3 Copy Number in Cancer

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Samples from unstained FFPE tissue on glass slides were manually microdissected, deparaffinized, and digested for 12 hours and isolated using the QIAamp genomic DNA isolation kit (QIAGEN). Metastatic (brain) and primary (breast) cancer tissues were assayed for gene copy number using TaqMan Gene Copy Number Assays. Each probe was designed based on a genomic sequence using Applied Biosystems proprietary Software. Each assay was run as a TaqMan real-time PCR reaction in triplicate, using a FAM-dye-based assay targeted to a genomic sequence YTHDF3 (Applied Biosystems, 4400291, ID: Hs00692696_cn) and a VIC dye-based assay for the reference gene, TaqMan™ Copy Number Reference Assay, human, RNase P (Applied Biosystems, 4403326). Each 20 μl PCR reaction contained 20 ng gDNA and TaqMan probe/primer Mix in TaqPath™ ProAmp Master Mixes, and was amplified using StepOnePlus™ Real-time PCR system (Applied Biosystems). Genomic DNAs of MDA-MB-231, MDA-MB-231Br, 4T1 and 4T1Br were analyzed for YTHDF3 copy number by using the above assay, with a targeted human or mouse genomic YTHDF3 respectively.
Chang G., Shi L., Ye Y., Shi H., Zeng L., Tiwary S., Huse J.T., Huo L., Ma L., Ma Y., Zhang S., Zhu J., Xie V., Li P., Han L., He C, & Huang S. (2020). YTHDF3 Induces the Translation of m6A-enriched Gene Transcripts to Promote Breast Cancer Brain Metastasis. Cancer cell, 38(6), 857-871.e7.
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3

Measuring KIR3DL1 and KIR3DS1 Gene Expression

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KIR3DL1 and KIR3DS1 GCN was measured using a quantitative PCR method and a comparative Ct method (ΔΔCt). The used amplification protocol, as well as primer and probe sequences, has been published by Jiang and coworkers (20 (link)). RNaseP was used as two copies reference gene (TaqMan Copy Number Reference Assay, human RNase P; Applied Biosystems).
Carlomagno S., Falco M., Bono M., Alicata C., Garbarino L., Mazzocco M., Moretta L., Moretta A, & Sivori S. (2017). KIR3DS1-Mediated Recognition of HLA-*B51: Modulation of KIR3DS1 Responsiveness by Self HLA-B Allotypes and Effect on NK Cell Licensing. Frontiers in Immunology, 8, 581.
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