Genemapper id x v1

Manufactured by Thermo Fisher Scientific

Sourced in United States, China

GeneMapper® ID-X v1.2 software is a data analysis tool designed for DNA fragment analysis. It provides the functionality to analyze, interpret, and manage DNA fragment data generated from genetic analyzers.

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61 protocols using genemapper id x v1

STR Profiling for Cell Line ID

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Nineteen short tandem repeat (STR) loci plus the gender-determining locus, amelogenin, were amplified using the commercially available EX20 Kit from AGCU (Cat. No. 600,010, Suzhou, China). A sample from the cell line was processed using the ABI Prism® 3500 Genetic Analyzer. The data were analyzed using GeneMapper® ID-X v 1.2 software (Applied Biosystems, Suzhou, China). Appropriate positive and negative controls were run and confirmed for each sample submitted.

Tu Y., Li L., Qin B., Wu J., Cheng T., Kang L, & Guan H. (2019). Long noncoding RNA glutathione peroxidase 3–antisense inhibits lens epithelial cell apoptosis by upregulating glutathione peroxidase 3 expression in age-related cataract. Molecular Vision, 25, 734-744.

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Authenticating Glioma Cell Lines

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The malignant human glioma cell line U87 was obtained from the American Type Culture Collection (Manassas, VA). LNZ308 was provided by Dr. Nicolas de Tribolet (Lausanne, Switzerland). Cell culture conditions of these cell lines were as previously described.^{16 (link)} Cell lines used in this study were authenticated using Short Tandem Repeat (STR) analysis by ATCC cell line authentication service (Manassas, VA). Samples were processed using the ABI Prism® 3500xl Genetic Analyzer and data was analyzed using GeneMapper® ID-X v1.2 software (Applied Biosystems, Foster City, CA). The genetic profiles for the samples were identical to the reported profile.

Premkumar D.R., Jane E.P., Thambireddy S., Sutera P.A., Cavaleri J.M, & Pollack I.F. (2017). Mitochondrial dysfunction RAD51, and Ku80 proteolysis promote apoptotic effects of Dinaciclib in Bcl-xL silenced cells. Molecular carcinogenesis, 57(4), 469-482.

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4Z-B-1 Cell Line Authentication

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The 4Z-B-1 cell line at P60 was authenticated by ATCC (ATCC sales order no. SO0546653). Seventeen STR loci plus the sex-determining locus amelogenin were amplified using the commercially available PowerPlex^® 18D Kit from Promega. The cell line sample was processed using the ABI Prism^® 3500xl Genetic Analyzer. The data were analyzed using GeneMapper^® ID-X v1.2 software (Applied Biosystems). Appropriate positive and negative controls were run and confirmed. The 4Z-B-1 cell line was not a match to any cell line in the ATCC, DSMZ or ExPASy databases.

Li Z., Zhuo W., Chen L., Zhang X., Chen C., Hu D., Chen Y., Yang J., Zhou Y., Mao M., Xu L., Ju S., Shen J., Wang Q., Dong M., Xie S., Zhou J, & Wang L. (2021). Establishment and Characterization of a HER2-Positive Cell Line Derived From the Pleural Effusion of a Drug-Resistant Breast Cancer Patient. Frontiers in Cell and Developmental Biology, 9, 680968.

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Cell Authentication by STR Profiling

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Cells were authenticated according to the protocol of the ATCC (Manassas VA, USA) based on 17 STR loci plus the gender-determining locus, amelogenin. Samples were processed with an ABI Prism 3500 × 1 Genetic Analyzer, and data were analyzed using GeneMapper IDX v.1.2 software (Applied Biosystems). Appropriate positive and negative controls were used, and the results were confirmed against ATCC and Deutsche Sammlung von Mikroorganismen und Zelkulturen (DSMZ) databases for each sample submitted (ATCC Sales Order No. SO0146233).

Zhou F., Zhang Y., Xu X., Luo J., Yang F., Wang L., Xie S., Sun J, & Yang X. (2018). Establishment and characterization of three stable Basal/HER2-positive breast cancer cell lines derived from Chinese breast carcinoma with identical missense mutations in the DNA-binding domain of TP53. Cancer Cell International, 18, 118.

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STR Profiling of Prostate Cancer Cell Lines

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Nineteen short tandem repeat (STR) loci plus the gender determining locus, amelogenin, were simultaneously co-amplified from PC-3M-1E8, PC-3M-2B4 and PC-3M cells using the EX20 kit (AGCU) according to the manufacture's protocol. The cell line samples were processed using the Prism 3500 Genetic Analyzer (Applied Biosystems) and the data were analyzed using GeneMapper ID-X v1.2 software (Applied Biosystems) by the Genetic Testing Biotechnology Corporation (Suzhou). Appropriate positive and negative controls were run and confirmed for each sample submitted. The resulting profile showed the assigned allele values corresponding to the number of repeat units identified for each locus. Cell lines were authenticated using STR analysis as described in ANSI Standard (ASN-0002) by the ATCC Standards Development Organization (SDO) in 2012.

Zhang S., Zheng C., Yao S., Wang Z., Xu L., Yang R., Meng X., Wu J., Zhou L, & Sun Z. (2018). Proteomic analysis of human prostate cancer PC-3M-1E8 cells and PC-3M-2B4 cells of same origin but with different metastatic potential. PLoS ONE, 13(10), e0206139.

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Multiplex STR Profiling of Cell Lines

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Seventeen short tandem repeat (STR) loci plus the gender determining locus, Amelogenin, were amplified using the commercially available PowerPlex^® 18D Kit from Promega. The cell line sample was processed using the ABI Prism^® 3500xl Genetic Analyzer. Data were analyzed using GeneMapper® ID-X v1.2 software (Applied Biosystems - ThermoFisher Scientific, Waltham, MA). Appropriate positive and negative controls were run and confirmed for each sample submitted. (ATCC Sales Order Number: SOJ32770).

Wang Y., Ding X., Wang S., Moser C.D., Shaleh H.M., Mohamed E.A., Chaiteerakij R., Allotey L.K., Chen G., Miyabe K., McNulty M.S., Ndzengue A., Knudson R.A., Greipp P.T., Clark K.J., Torbenson M.S., Kipp B.R., Zhou J., Barrett M.T., Gustafson M.P., Alberts S.R., Borad M.J, & Roberts L.R. (2016). Antitumor effect of FGFR inhibitors on a novel cholangiocarcinoma patient derived xenograft mouse model endogenously expressing an FGFR2-CCDC6 fusion protein. Cancer letters, 380(1), 163-173.

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STR Loci Analysis Using GeneMapper

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Short tandem repeat (STR) loci were analyzed in Cosmo genetech (Seoul, Korea) using GeneMapper® ID-X v1.2 software (Applied Biosystems, Suzhou, China). Appropriate positive and negative controls were run and confirmed for each sample submitted. The STR analyses are presented in Appendix 1.

Yoo K., Son B.K., Kim S., Son Y., Yu S.Y, & Hong H.S. (2017). Substance P prevents development of proliferative vitreoretinopathy in mice by modulating TNF-α. Molecular Vision, 23, 933-943.

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Generating Artificial Degraded DNA Samples

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To obtain the artificial single-source degraded DNA, the DNA with the highest heterozygosity from the 32 samples was incubated at 98°C for 35, 40, and 45 min in the Eppendorf 6331 Nexus Gradient Flexlid Thermal Cycler (Eppendorf, Hamburg, Germany). In addition, the standard DNA M308 was incubated in a PCR system at 98°C for 120, 160, and 170 min.
To obtain artificially mixed and degraded DNA, the two DNA samples with the highest degree of heterozygosity and homozygosity from the 32 samples were mixed and then subjected to a series of dilutions (1:1, 1:10, 1:20, 1:50, 1:100, 1:500, and 1:1,000) and incubated at 98°C for 35, 40, and 45 min.
The degree of DNA degradation after incubation was determined using a High Sensitivity DNA Kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, United States) and the AGCU EX22 Kit (Applied ScienTech, Jiangsu, China) on an ABI 3500 Genetic Analyzer (Applied Biosystems), according to the manufacturers’ instructions. The results were analyzed using the GeneMapper ID-X v1.2 software (Applied Biosystems).

Zhang R., Tan Y., Wang L., Jian H., Zhu J., Xiao Y., Tan M., Xue J., Yang F, & Liang W. (2022). Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing. Frontiers in Genetics, 12, 800598.

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STR Profiling of Cell Line

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Nineteen short tandem repeat (STR) loci plus the gender-determining locus, amelogenin, were amplified using the commercially available EX20 Kit from AGCU (Wuxi, China). The cell line sample was processed using the ABI Prism® 3500 Genetic Analyzer. Data were analyzed using GeneMapper® ID-X v1.2 software (Applied Biosystems, Suzhou, China). Appropriate positive and negative controls were run and confirmed for each sample submitted. The STR analyses are presented in Appendix 1.

Wang Y., Sang A., Zhu M., Zhang G., Guan H., Ji M, & Chen H. (2016). Tissue factor induces VEGF expression via activation of the Wnt/β-catenin signaling pathway in ARPE-19 cells. Molecular Vision, 22, 886-897.

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PowerPlex®18D STR Profiling Protocol

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Seventeen STR loci plus Amelogenin were amplified using the PowerPlex®18D Kit (Promega). Samples were processed using the Prism®3500xl Genetic Analyzer and data were analysed with GeneMapper®ID-X v1.2 software (Applied Biosystems). Appropriate positive and negative controls have been used.

Rabino M., Rurali E., Zamboni C., Rovina D., Mallia S., Cauteruccio M., Baggiano A., Giacari C.M., Bellin M, & Pompilio G. (2023). Generation of four human induced pluripotent stem cell lines from COVID-19 hospitalized patients with increased levels of cardiac Troponin in the acute infection phase developing or not myocarditis. Stem Cell Research, 67, 103018.

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