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Short tandem repeat profiling

Manufactured by Promega
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Short tandem repeat profiling is a technique used to analyze the number of short, repeated DNA sequences within a genetic sample. It provides a detailed genetic fingerprint that can be used for various applications, such as human identification and forensics.

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7 protocols using short tandem repeat profiling

1

Culturing Diverse Cell Lines and Primary Macrophages

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MDA-MB-231 human breast carcinoma cells expressing GFP (MDA231) were kindly provided by Dr. Frank Gertler, MIT. PC3 human prostate carcinoma cells (PC3), MDA-MB-435S human melanoma cells (MDA435), and Raw 264.7 mouse macrophages (Raw) were obtained from American Type Culture Collection. MDA231, MDA435, and Raw cells were cultured in DMEM. PC3 were cultured in RPMI. All media were supplemented with 10% fetal bovine serum (FBS), and 100 U/mL penicillin/streptomycin. Cell lines were authenticated using Short Tandem Repeat profiling (Promega).
To generate primary bone marrow-derived macrophages (BMDM), bone marrow cells were first isolated from the femurs of C57BL/6 mice. These cells were then differentiated in RPMI supplemented with 10% FBS, 1% HEPES, 40 ng/mL MCSF (Peprotech) and 50 µM β-Mercaptoethanol for 7 days to produce BMDM. Primary human monocyte-derived macrophages (MDMΦ) were generated from monocytes isolated from whole blood (Research Blood Component) using a Ficoll-Paque gradient and the EasySep™ Monocyte Enrichment Kit (StemCell Tech.). These cells were cultured with IMDM supplemented with 2% L-glutamine and AB serum for 7 days to generate MDMΦ. All cells were cultured in a humidified incubator at 5% CO2 and 37 °C.
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2

Melanoma Cell Culture and Isolation

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SKMEL-28 and A375 cell lines were obtained from American Type Culture Collection (Rockville, MD), and further authenticated by short tandem repeat profiling (Promega). Cells were monitored for mycoplasma contamination every 6 months. All cell lines were grown in Dulbeccos Modified Eagles Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), Penicillin (100 U/mL), and Streptomycin (100 μg/mL). Cells were incubated at 37°C at 5% CO2 and sub-cultured every 72 hours. ALDHhigh cells were isolated by fluorescence-activated cell sorting (FACS) and were grown in DMEM/F-12 serum-free media containing 1 × N-2 Supplement (Gibco) 10 ng/mL basic fibroblast growth factor (Gibco), and 10 ng/mL epidermal growth factor (Gibco). For soft agar assays, DMEM media (Invitrogen) powder was reconstituted in ultrapure water (500 mL) and supplemented with 20% FBS, Penicillin (200 U/mL), and Streptomycin(200 μg/mL).
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3

Isolation and Culture of NSCLC Cell Lines

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Human NSCLC cell lines were obtained by the American Type Culture Collection (ATCC, Manassas, Virginia, USA) and were cultured in RPMI-1640 (Sigma-Aldrich) medium which was supplemented with 10% foetal bovine serum (FBS; Life Technologies, Gaithersburg, Maryland, USA) in a humidified atmosphere with 5% CO2. The identity of cell lines was confirmed by Short tandem repeat profiling (Promega). Cetuximab, atezolizumab and panitumumab were purchased from Selleck Chemicals (Munich, Germany). Avelumab, was provided by Merck (Darmstadt, Germany), as part of a Cooperative Research and Development Agreement. Peripheral blood mononuclear cells (PBMCs) from healthy donors (HD) or from NSCLC patients were isolated by Ficoll-Paque Plus (GE Healthcare). NK cells were obtained through magnetic separation by using the NK CELL isolation kit, HUMAN (Miltenyi Biotech 130-092-657) according to the manufacturer’s protocol.
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4

Establishment of CNX-2006-Resistant HCC827 Cells

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HCC827CNXR S1 and S4 cells were established by stepwise exposure of HCC827EPR cells to increasing concentration of CNX‐2006 (50 nmol/L–1 μmol/L) for 4 months as described previously.19 Resultant cells were subsequently subcloned by limiting dilution in 96‐well plates. As a result, only HCC827CNXR S1 and S4 cells were available for the present study. Cell identity of these cell lines were confirmed by cell line authentication service using short tandem repeat profiling (Promega, Madison, WI, USA).
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5

Breast Cancer Cell Line Models

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MCF7 and HCC1428 cells were obtained from the American Type Culture Collection (ATCC, Rockville, USA) and cultured in phenol red-free RPMI1640 medium supplemented with 10% fetal bovine serum and 1nM estradiol (E2). All cell lines were banked in multiple aliquots to reduce the risk of phenotypic drift and identity confirmed by short tandem repeat profiling (Promega, Madison, WI, USA). Long-term-estrogen-deprived cells (MCF7-LTED and HCC1428-LTED) modelling resistance to an AI were cultured in phenol red free RPMI 1640 supplemented with 10% DCC-FBS [14 (link)]. MCF7-TAMR and matched MCF7 cells were maintained in DMEM-F12 lacking phenol red and supplemented with 1% FBS and containing 100nM 4OHT, as previously described [15 (link), 16 (link)]. The parental cell line was referred to as 1%MCF7 and is a recognised model which is refractory to E2 but sensitive to tamoxifen and fulvestrant [15 (link), 17 (link)], HCC1428-TAMR were cultured in the presence of 0.01nM E2 and 100nM 4-OHT. Cells were stripped of E2 or 4-OHT for 3 days prior to experimentation.
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6

Visualizing ER and Golgi dynamics

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HeLa cells (RIKEN BioResource Research Center, #RCB0007) were cultured and transfected as described previously (Tojima et al., 2023 (link)). Cell line identity was verified by short tandem repeat profiling (Promega) and cells were negative for mycoplasma contamination (MycoStrip, Invivogen). Expression plasmids encoding EGFP-Sec16B, mCherry-KDEL, and EGFP-Rab1 were obtained from Addgene (#66607, #55041, and #49467 respectively). Plasmids encoding iRFP-ST, EGFP-ERGIC53, and mScarlet-I-GRASP65 under the control of CMV promoter were generated from mCherry-ST (Addgene, #55133), iRFP713 (Addgene, #31857), pMXs-IP spGFP-ERGIC53 (Addgene, #38270), EGFP-GRASP65 (Addgene, #137709), and mScarlet-I-Giantin (Addgene, #85050) using In-Fusion Cloning kit (Takara).
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7

Cell Culture and Characterization Protocol

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The human cSCC A431 cell line56 (link) and normal human primary dermal fibroblasts (NHDFs) were purchased from the American Type Culture Collection (ATCC). The human cSCC DJM-1 cells were separated from human cSCC57 (link). All of the cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Nacalai Tesque, Kyoto, Japan) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, Germany). These cells were maintained in a humidified cell incubator containing 5% CO2 with temperature set at 37 °C. Each cell line was confirmed by short tandem repeat profiling (Promega, WI, USA) in August 2018 and was utilized in less than 6 months of unceasing passage. All cells were verified for the absence of Mycoplasma contamination (Venor®GeM Classic, Minerva Biolabs, NJ, USA).
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