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Ampf str identifier kit

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The AmpF/STR Identifier Kit is a DNA amplification kit used for forensic and human identification applications. It is designed to generate a DNA profile from biological samples. The kit includes reagents and primers necessary for the amplification of specific genetic markers.

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Lab products found in correlation

Fetal bovine serum (fbs), by Thermo Fisher Scientific (3 mentions) Dulbecco modified eagle medium (dmem), by Thermo Fisher Scientific (3 mentions) Kuramochi cell line, by Japanese Collection of Research Bioresources Cell Bank (3 mentions) Ovcar5, by American Type Culture Collection (3 mentions) Hct116, by American Type Culture Collection (2 mentions) Sw480, by American Type Culture Collection (2 mentions) Sw620, by American Type Culture Collection (2 mentions) Sw948, by American Type Culture Collection (2 mentions) Lncap, by American Type Culture Collection (2 mentions) Amd3100, by Selleck Chemicals (2 mentions) Enz mdv3100, by Selleck Chemicals (2 mentions) Caov3, by American Type Culture Collection (2 mentions) Ovcar8, by American Type Culture Collection (2 mentions) Bt549, by American Type Culture Collection (1 mentions) Mda mb 231, by American Type Culture Collection (1 mentions) Skov3, by American Type Culture Collection (1 mentions) Ovcar3, by American Type Culture Collection (1 mentions) Dld1 colon cancer cells, by American Type Culture Collection (1 mentions) 1640 medium, by Thermo Fisher Scientific (1 mentions) Mcf 7, by National Collection of Authenticated Cell Cultures (1 mentions)

Spelling variants of this product

Identifier Kit (4 citations) AmpF/STR® Identifier® PCR Amplification kit (4 citations) STR) Identifier kit (2 citations)

29 protocols using ampf str identifier kit

1

Characterization of Breast Cancer Cell Lines

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The BT-549, MDA-MB-231, 4T1, and EMT-6 breast cancer cell lines were obtained from ATCC. Human breast cancer cell lines and mouse cancer cell lines were cultured in Dulbecco's modified Eagle's medium/F12 and Dulbecco's modified Eagle's medium, respectively, supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic mixture. All cell lines tested negative for mycoplasma contamination and validated by short-term repeat DNA fingerprinting with use of the AmpF_STR identifier kit according to the manufacturer’s protocol (Applied Biosystems, #4322288) at The University of Texas MD Anderson Cancer Center.
Cha J.H., Chan L.C., Wang Y.N., Chu Y.Y., Wang C.H., Lee H.H., Xia W., Shyu W.C., Liu S.P., Yao J., Chang C.W., Cheng F.R., Liu J., Lim S.O., Hsu J.L., Yang W.H., Hortobagyi G.N., Lin C., Yang L., Yu D., Jeng L.B, & Hung M.C. (2022). Ephrin receptor A10 monoclonal antibodies and the derived chimeric antigen receptor T cells exert an antitumor response in mouse models of triple-negative breast cancer. The Journal of Biological Chemistry, 298(4), 101817.
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2

Cell Line Sourcing and Validation

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Cell lines obtained from ATCC include: EL4 (2009), NALM-6 (2011), U87 (2012), T98G (2012), LN18 (2012) and A431 (2012). K562 clone 9 were generated by stable expression of 41BB-L, CD86, CD64 and tCD19 (18 (link)) and were a kind gift from Dr. Carl June (University of Pennsylvania), obtained in 2007. U87-172b cells, designated U87high in this study, overexpressing wild-type EGFR were a kind gift from Dr. Oliver Bolger (MDACC) and obtained in 2012. Human renal cortical epithelial (HRCE) cells were obtained from Lonza in 2012. Details of propagation and genetic modification are described in Supplementary Materials and Methods. All cell line identities were validated by STR DNA fingerprinting in 2012, at the time of the study, using the AmpF_STR Identifier kit according to manufacturer’s instructions (Applied Biosystems, cat #4322288). The STR profiles were compared to known ATCC fingerprints (ATCC.org), and to the Cell Line Integrated Molecular Authentication database (CLIMA) version 0.1.200808 (19 (link)). The STR profiles matched known DNA fingerprints.
Caruso H.G., Hurton L.V., Najjar A., Rushworth D., Ang S., Olivares S., Mi T., Switzer K., Singh H., Huls H., Lee D.A., Heimberger A.B., Champlin R.E, & Cooper L.J. (2015). Tuning sensitivity of CAR to EGFR density limits recognition of normal tissue while maintaining potent anti-tumor activity. Cancer research, 75(17), 3505-3518.
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3

Establishment and Validation of Ovarian Cancer Cell Lines

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The SKOV3 (catalog no. HTB-77) and OVCAR3 (catalog no. HTB-161) ovarian cancer cell lines were obtained from American Type Culture Collection (ATCC). The OVCA433 and OVCA420 ovarian cancer cell lines were obtained from A.K.S.’s lab (MD Anderson Cancer Center). SKOV3, OVCAR3, OVCA433 and OVCA420 were cultured in Dulbecco’s modified Eagle’s medium/F12 supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic mixture containing 100 units ml−1 of penicillin and 100 mg ml−1 of streptomycin (P/S). The DOV13 and A2780 ovarian cancer cell lines were obtained from A.K.S.’s lab and maintained in RPMI medium containing 10% FBS and 1% P/S. The SUM149 (catalog no. CS-07) TNBC cell line was obtained from Asterand Biosciences and maintained in F12K medium containing 5% FBS, 10 mM Hepes, 1 mg ml−1 of hydrocortisone, 5 µg ml−1 of insulin and 1% P/S. All cell lines were validated by short tandem repeat (STR) DNA fingerprinting using the AmpF_STR identifier kit following the manufacturer’s protocol (Applied Biosystems, catalog no. 4322288). The STR profiles were compared with ATCC fingerprints (ATCC.org) and the Cell Line Integrated Molecular Authentication database v.0.1.200808 (http://bioinformatics.istge.it/clima/)57 (link). The PARP inhibitor-resistant TNBC cell lines nos. 6 and 15 were obtained by exposing the SUM149 TNBC cell line to increasing concentrations of talazoparib.
Chu Y.Y., Chen M.K., Wei Y., Lee H.H., Xia W., Wang Y.N., Yam C., Hsu J.L., Wang H.L., Chang W.C., Yamaguchi H., Jiang Z., Liu C., Li C.F., Nie L., Chan L.C., Gao Y., Wang S.C., Liu J., Westin S.N., Lee S., Sood A.K., Yang L., Hortobagyi G.N., Yu D, & Hung M.C. (2022). Targeting the ALK–CDK9-Tyr19 kinase cascade sensitizes ovarian and breast tumors to PARP inhibition via destabilization of the P-TEFb complex. Nature Cancer, 3(10), 1211-1227.
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4

Characterization of Metastatic Cancer Cell Lines

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DLD1 colon cancer cells and AsPC1 pancreatic cancer cells were obtained from the American Type Culture Collection (ATCC). AsPC1 is morphologically heterogenous in culture by phase contract microcopy. LS-LiM6 and L3.6pl are metastatic cell lines selected for increased liver metastasizing ability by serial in vivo passaging following orthotropic implantation in athymic nude mice. LS-LiM6 colon cancer cells were derived from human colon cancer cell line LS174T31 (link) and L3.6pl pancreatic cancer cells were derived from the COLO357 pancreatic cancer cell line.11 (link) Cell lines were validated by STR DNA fingerprinting using the AmpF_STR Identifier kit according to the manufacturer's instructions (Applied Biosystems, Foster City, CA, USA, cat 4322288). The STR profiles were compared to known ATCC fingerprints (ATCC.org), and to the Cell Line Integrated Molecular Authentication database (CLIMA) version 0.1.200808 (http://bioinformatics.istge.it/clima/). The STR profiles matched known DNA fingerprints of LS174T colon cancer cells. Cells were maintained at 37°C in a 5% CO2 atmosphere in Dulbecco's modified Eagle medium containing 10% heat-inactivated fetal bovine serum with penicillin and streptomycin.
Ilmer M., Mazurek N., Byrd J.C., Ramirez K., Hafley M., Alt E., Vykoukal J, & Bresalier R.S. (2016). Cell surface galectin-3 defines a subset of chemoresistant gastrointestinal tumor-initiating cancer cells with heightened stem cell characteristics. Cell Death & Disease, 7(8), e2337-.
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5

Cell Line Cultivation and Authentication

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Human MCF-7 and T-47D breast cancer cell lines were purchased from the China Center for Type Culture Collection (Wuhan, China). Cell lines were cultured in Dulbecco's Modified Eagle's Medium (DMEM) or Roswell Park Memorial Institute (RPMI) 1640 Medium (Gibco, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, USA) and 1% antibiotics (100 U/mL penicillin and 0.1 mg/mL streptomycin) at 37°C in a humidified atmosphere of 5% CO2. DNA sequencing using an Applied Biosystems AmpF/STR Identifier kit was performed to test all cell lines routinely and cell lines were tested for free from mycoplasma infection (MycoAlert, USA).
Gong Y., Hu N., Ma L., Li W., Cheng X., Zhang Y., Zhu Y., Yang Y., Peng X., Zou D., Tian J., Yang L., Mei S., Wang X., Lo C.H., Chang J., Hou T., Zhang H., Xu B., Zhong R, & Yuan P. (2020). ABTB2 Regulatory Variant as Predictor of Epirubicin-Based Neoadjuvant Chemotherapy in Luminal A Breast Cancer. Frontiers in Oncology, 10, 571517.
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6

Functional Analysis of rs12880540 and miR-3122

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To further examine whether rs12880540 could have impact on the binding of miR‐3122 and LINC00520, predicted by lncRNASNP2 database (Figure S1), 293T cell lines were obtained and grown in DMEM supplemented with 10% fetal bovine serum (GIBCO) in a humidified atmosphere of 5% CO2 at 37°C. All cell lines were never subcultured for more than 3 months and sequenced by DNA using the Applied Biosystems Amp F/STR Identifier kit and last performed in September 2018. The miR‐3122 mimics and negative control (NC) were synthesized in Genecreate. For transfection assays, 293T cells were seeded in 48‐well plates and simultaneously transfected with PGL3‐basic‐luc vector and miR‐3122 or NC mimics using Lipofectamine 3000 (Invitrogen). After 48 hours, cells were harvested, and Renilla luciferase/Firefly luciferase activities between different alleles were detected and analyzed according to the manufacturer's instruction (dual luciferase assay system, Promega). All experiments were performed independently in triplicate.
Guo Q., Xu L., Peng R., Ma Y., Wang Y., Chong F., Song M., Dai L, & Song C. (2020). Characterization of lncRNA LINC00520 and functional polymorphisms associated with breast cancer susceptibility in Chinese Han population. Cancer Medicine, 9(6), 2252-2268.
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7

Culturing and Characterizing CRC Cell Lines

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The human CRC cell lines HCT116, DiFi, HCT8, HT29, LoVo, RKO, DLD-1, SW620, SW480, Caco-2, SW1463, T84, and SW948, the normal human intestinal epithelial cell line HIEC, CTX-sensitive CC cells and CTX-resistant CC-CR cells have been previously described 11 (link) and were cultured in DMEM (Gibco) with 10% fetal calf serum (Gibco), 1% antibiotic-antimycotic (Gibco), 1% L-glutamine and 1% MEM nonessential amino acids (Gibco) at 37°C in 5% CO2. The complete medium used for culturing CC-CR cells contained 3 µg/ml CTX (Merck). The cell lines were recently authenticated by cellular morphology and short tandem repeat analysis using the AmpF/STR Identifier Kit (Applied Biosystems). All cells were tested for mycoplasma every 3 months and were negative. Cells with negative detection results were passaged 3 days after thawing and then frozen for long-term storage. All experiments involving the cell lines were performed within five passages. The 3D culture protocol has been previously described 11 (link). Colonies of CC and CC-CR cells were lysed for RNA extraction after 14 days or fixed in 4% paraformaldehyde (PFA) for counting (Oxford Optronix GelCount) after 21 days. Origin and genetic information of cell lines used in the study is listed in Table S1.
Sun L., Fang Y., Wang X., Han Y., Du F., Li C., Hu H., Liu H., Liu Q., Wang J., Liang J., Chen P., Yang H., Nie Y., Wu K., Fan D., Coffey R.J., Lu Y., Zhao X, & Wang X. (2019). miR-302a Inhibits Metastasis and Cetuximab Resistance in Colorectal Cancer by Targeting NFIB and CD44. Theranostics, 9(26), 8409-8425.
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8

Breast Cancer Tissue and Cell Line Analysis

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Two independent sets of breast cancers with matched protein lysates and formalin-fixed, paraffin-embedded (FFPE) sections were utilized: TCGA (n = 885) and MDACC (n = 63). For the TCGA cohort, only a subset of cases with RPPA data was available with matched unstained FFPE sections (n = 109).
Breast cancer cell lines (T47D, MCF7) were obtained from the MD Anderson Characterized Cell Line Core facility (Houston, TX). The identities of all cell lines were verified using AmpF/STR Identifier kit (Applied Biosystems) by the core facility and used within 6 months of obtaining the cell lines. The lines were cultured in DMEM supplemented with 5% fetal bovine serum (FBS) at 37°C in 5% carbon dioxide atmosphere. Cell lines were routinely tested for Mycoplasma infection using a MycoTect Kit (Invitrogen).
MDA-MB-134 (ATCC) and Sum44PE (Asterand) cells were cultured as previously described (16 (link)). The cell lines were authenticated annually by PCR RFLP analyses and confirmed to be Mycoplasma negative at the University of Pittsburgh Cell Culture and Cytogenetics Facility (Pittsburgh, PA).
Cancer tissues from the University of Utah (A.W.) were mastectomy specimens from patients without prior therapy. Normal specimens were collected from matched grossly uninvolved tissues. Tissues were collected and de-identified using approved IRB#10924.
Dennison J.B., Shahmoradgoli M., Liu W., Ju Z., Meric-Bernstam F., Perou C.M., Sahin A.A., Welm A., Oesterreich S., Sikora M.J., Brown R.E, & Mills G.B. (2016). High intra-tumoral stromal content defines Reactive breast cancer as a low-risk breast cancer subtype. Clinical cancer research : an official journal of the American Association for Cancer Research, 22(20), 5068-5078.
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9

Culturing and Authenticating CRC Cell Lines

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The CRC cell lines SW480, SW948, HCT116 and SW620 and the human intestinal epithelial cell line HIEC were procured from the American Type Culture Collection and maintained in DMEM (HyClone, Fisher Scientific) supplemented with 10% foetal bovine serum, streptomycin (100 μg/mL) and penicillin (100 units/mL) in a 5% (v/v) CO2 humidified atmosphere at 37°C. Cellular morphology and short tandem repeat analyses were conducted to authenticate all cell lines using an AmpF/STR Identifier Kit (Applied Biosystems).
Du F., Li Z., Zhang G., Shaoyan S., Geng D., Tao Z., Qiu K., Liu S., Zhou Y., Zhang Y., Gu J., Wang G., Li L, & Wu W. (2020). SIRT2, a direct target of miR‐212‐5p, suppresses the proliferation and metastasis of colorectal cancer cells. Journal of Cellular and Molecular Medicine, 24(17), 9985-9998.
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10

Genetic Mouse Model Cell Lines for Ovarian Cancer Research

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The K-ras/PTEN cell line were established by us from ovarian tumors generated using a genetic mouse model.17 (link) The SKOV3ip1 and HeyA8 cell lines were provided by Dr. Gordon Mills (MD Anderson Cancer Center, Houston, TX). The IOSE 397 cell line was kindly shared by Dr. Nelly Auersperg (University of British Columbia, Canada). The IGROV1 and Ovcar-5 cell lines were purchased from American Type Culture Collection (ATCC). The Kuramochi cell line was purchased from the Japanese Collection of Research Bioresources Cell Bank. Cell lines were validated by short tandem repeat (STR) DNA fingerprinting using the AMPF’STR Identifier kit (Applied Biosystems) and compared with ATCC and University of Texas MD Anderson Cancer Center fingerprints. Metformin obtained from Sigma-Aldrich (St Louis, MO). The Cdk4, cyclin D1, AMPK, EGFR, ErbB4, PDGFRα, FABP4 and FASN antibodies were from Cell Signaling Technologies (Beverly, MA) and the cyclin D1 antibody used for immunohistochemistry was from Novus Biologicals (Littleton, CO). The LKB1 and ACC antibodies were from Millipore (Billerica, MA), PARP 1/2 was from Santa Cruz Biotechnology (Santa Cruz, CA), FASN was from ATLAS (Stockholm, Sweden), phosphorylated RON was from R&D Systems (Minneapolis, MN), and RON was from Epitomics (Burlingame, CA).
LENGYEL E., LITCHFIELD L.M., MITRA A.K., NIEMAN K.M., MUKHERJEE A., ZHANG Y., JOHNSON A., BRADARIC M., LEE W, & ROMERO I.L. (2014). Metformin inhibits ovarian cancer growth and increases sensitivity to paclitaxel in mouse models. American journal of obstetrics and gynecology, 212(4), 479.e1-479.e10.
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