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217 protocols using f7524

1

Cell Line Cultivation Protocols for Germ-Cell Tumor, Leukemia, Hepatocellular Carcinoma, and Embryonic Kidney

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The human testicular germ-cell tumor cell line 833K [24 (link),25 (link)] was a generous gift from Dr. Anne Karin Olsen (Norwegian Institute of Public Health, Oslo, Norway). These cells were grown in RPMI 1640 media (Thermo Fisher Scientific, 21875) with 10% fetal bovine serum (FBS; Thermo Fisher Scientific, 10099141) and 1% penicillin-streptomycin (P/S; Thermo Fisher Scientific, 15140122). HAP1 (derived from male chronic myelogenous leukemia cell line KBM-7) cell line (Horizon Discovery, wild type C631, ENDOV- HZGHC002792c012) was grown in IMDM media (Merck, I6529) with 10% FBS (Merck, F7524) and 1% P/S. The hepatocyte derived cellular carcinoma cell line Huh-7 (Health Science Research Resources Bank, JCRB0403) was grown in DMEM, low glucose media (Thermo Fisher Scientific, 22320) with 10% FBS (Merck, F7524) and 1% P/S. The human embryonic kidney cell line HEK 293T (American type Culture Collection (ATCC), CRL-11268) was grown in DMEM, high glucose, GlutaMAX(TM) media (Thermo Fisher Scientific, 10566) with 10% FBS (Merck, F7524) and 1% P/S. The human monocytic cell line THP-1 (ATCC, TIB-202) was grown in RPMI 1640 media (Biowest, L0496–500) supplemented with 10% FBS (Merck, F7524) and 1% P/S (Merck, P4458). All cells were kept at 37 °C and 5% CO2.
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Cell Culture Conditions for Proliferation Assays

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HCT116 cells were purchased from ATCC (#CCL-247) and cultured in DMEM with 10% heat inactivated fetal calf serum (FCS) (SigmaAldrich #F7524) and 1% L-Glutamine (LifeTech Austria/Invitrogen #25030024). HCT116 cells are near-diploid, chromosomally stable (P53 wild-type) and do not elicit interferon response upon reporter plasmid transfection6 (link). For proliferation assays, cells were seeded into 6-well plates with 2x105 cells/well starting seeding density with or without the addition of Indole-3-acetic acid sodium salt (IAA/auxin, SigmaAldrich #I5148-2G) 500 μM final concentration. For up to 5 consecutive days cells were counted (Countess II Thermo Fisher #AMQAX1000) in 24 h intervals. K562 BRD4-AID cells were obtained from ref. 33 (link) and cultured in RPMI-1640 with 10% FCS (SigmaAldrich #F7524). CH12 mouse lymphoma cell lines (wild-type and knock-out for different Mediator subunits) were obtained from ref. 18 (link) and were cultured in RPMI-1640 with 10% FCS (SigmaAldrich #F7524), 1% Penicillin-Streptomycin and 50 μM of β-mercaptoethanol (Thermo Fisher Scientific). All cell lines tested negative for mycoplasma.
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Culturing Human Dermal Fibroblasts and HEK293FT Cells

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Human primary dermal fibroblasts were isolated from a skin biopsy65 (link) obtained from a healthy 30-year-old female. Fibroblasts were cultured in DMEM (61965-059, Gibco) supplemented with 15% FBS (F7524, BCBZ9153, Sigma), 1% non-essential amino acids (NEAA, 11140035, Gibco), 1% penicillin–streptomycin (P/S, 15140122, Gibco) and maintained at 37 °C in humidified atmosphere with 5% CO2. Cells were cultured for not more than 1 month. Human HEK293FT cells (gently provided by Prof. Barile, University of Southern Switzerland, Switzerland) were cultured in DMEM with 10% FBS (F7524, 0001643900 Sigma), 1% NEAA and 1% P/S.
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Culturing and Maintaining Primary Neuronal Cells

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All cells were cultured in a humidified incubator at 37°C and 5% CO2. HEK293T (American Type Culture Association (ATCC)) and H4 cells (a gift from Dr Helen Scott and Professor James Uney) were maintained in DMEM (D5796; Sigma-Aldrich) supplemented with 10% foetal bovine serum (F7524; Sigma-Aldrich). For the GFP/RFP-based immunoprecipitations, HEK293T cells were transfected with GFP/RFP- expressing constructs using polyethyleneimine (PEI) (Sigma-Aldrich). BHK-21 cells (ATCC) were maintained in Alpha MEM (22561–021, Gibco) supplemented with 5% foetal bovine serum (F7524; Sigma-Aldrich) and 1% Penicillin/Streptomycin (P0781, Sigma-Aldrich).
Primary neuronal cultures were prepared from embryonic day E18 Wistar rat brains as previously described (Martin and Henley, 2004 (link)). In brief, dissociated cortical cells were grown in six well dishes (500,000 cells/well), and hippocampal cells on 22 mm glass coverslips (150,000 cells/coverslip) coated with poly-L-lysine (P2636; Sigma-Aldrich) in 2 ml plating medium (Neurobasal medium (21103–049, Gibco) supplemented with 5% horse serum (H1270), 2% B27 (17504–044, Gibco) and 1% Glutamax (35050–038)) which was exchanged for 2 ml feeding medium 2 hr after plating (Neurobasal medium (21103–049, Gibco), 2% B27 (17504–044, Gibco), and 0.4% Glutamax (35050–038)). Cells were then fed with an additional 1 ml of feeding medium 7 days after plating.
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Cell Culture Conditions for Cell Lines

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A549 and HL-60 cells were from ATCC. Nalm-6 topoisomerase knock-out cells, originally obtained by Noritaka Adachi (Yokohama City University, Japan), were kindly provided by Caroline Austin and Ian Cowell (Newcastle University, UK). CHO-AA8, CHO-K1 and V79 cells, along with their DNA repair deficient variants, were provided by Malgorzata Zdzienicka (Leiden University, Netherlands). A549, HL-60, Nalm-6 and derived cells were cultured in RPMI-1640 medium (Corning 15-040-CV); CHO-K1, CHO-AA8 and all derived cells were cultured in F-10 Ham medium (Corning 10-070-CV). Media were supplemented with 10% FBS (Sigma–Aldrich F7524) and antibiotics: penicillin (60 μg/ml) and streptomycin (42.4 μg/ml). LoVo/DX cells were cultured in 1:1 (v/v) mixture of RPMI-1640 and Opti-MEM (both IIET, Wroclaw, Poland) supplemented with 5% FBS (F7524), 2 mM L-glutamine (G8540), 1mM sodium puryvate (P4562) (all Sigma-Aldrich, Poznan, Poland), 0.1 μg/ml doxorubicin (Medac GmbH, F130421A) and antibiotics: penicillin (60 μg/ml) and streptomycin (100 μg/ml). All cells were maintained at 37°C in humidified atmosphere of 5% CO2 and 95% air and routinely screened for Mycoplasma contamination.
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Cell Culture Protocols for Multiple Cell Lines

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HEK293T, HEK293, control HEK293, STT3A-/- HEK293, STT3B-/- HEK293, COS-7, NIH/3T3, and RAW 264.7 EROS FLAG-tagged cells were maintained in DMEM medium (21969035, Thermo Fisher) containing 10% FBS (F7524, Sigma-Aldrich) and 100 U/mL of Penicillin-Streptomycin-Glutamine (10378016, Thermo Fisher). PLB985 (ACC 139, DSMZ), PLB-clone 14 (Thomas et al., 2018b (link)), PLB- clone 20 (Thomas et al., 2018b (link)), and PLB985 overexpressing EROS- GFP lentivirus construct were cultured in complete RPMI medium consisting of RPMI 1640 (31870025, Thermo Fisher), 10% FBS (F7524, Sigma-Aldrich), 2 mM GlutaMAX (35050061, Thermo Fisher), 1 mM sodium pyruvate (11360070, Thermo Fisher); 0.5 mg/mL Penicillin-Streptomycin-Glutamine (10378016, Thermo Fisher), and 20 mM HEPES (H3537, Sigma-Aldrich). HEK293-F cells were grown in suspension using FreeStyle medium (Invitrogen). All cell lines were tested and confirmed mycoplasma-free using the protocol for Myco-Alert Mycoplasma Detection Kit (LT07-218, Lonza).
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Culturing of Osteoblast and Fibroblast Cells

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hFOB 1.19 cells (ATCC, Manassas, VA, USA, CRL-1137) were maintained in DMEM/Ham’s F-12 medium without phenol red (Sigma–Merck, Darmstadt, Germany, D6434) supplemented with 10% FBS (Sigma, F7524), 2.5 mM of L-glutamine (Sigma, G7513), and the selection reagent, G418 (Sigma, G8168), at a final concentration of 0.3 mg·mL−1 at 34 °C, 5% CO2, and 100% relative humidity. Cells were passaged regularly when sub-confluent using a trypsin-EDTA solution without phenol red (Gibco, 15400054, Thermo Fisher Scientific, Waltham, MA, USA).
Murine fibroblasts L929 (ATCC CCL-1) were maintained in an MEM (Sigma, M0446) medium supplemented with 10% FBS (FBS, Sigma F7524) under standard conditions of 37 °C, 5% CO2 and 100% relative humidity. Cells were passaged regularly when sub-confluent using trypsin-EDTA solution (Sigma, T4049).
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Culturing Human Prostate Cell Lines

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The human PCa cell lines LNCaP, 22Rv1, and PC3 were purchased from the Stem Cell Bank, Chinese Academy of Sciences (Shanghai, China) and cultured in RPMI-1640 medium (L220KJ; BasalMedia, Shanghai, China) with 10% (v/v) fetal bovine serum (F7524; Sigma, St. Louis, MO, USA). The human PCa cell lines DU145 were purchased from the Stem Cell Bank, Chinese Academy of Sciences (Shanghai, China) and cultured in DMEM high glucose medium (L110KJ; BasalMedia, Shanghai, China) with 10% (v/v) fetal bovine serum (F7524; Sigma, St. Louis, MO, USA). The prostate normal cell lines BPH-1 and RWPE-1 were purchased from the Stem Cell Bank, Chinese Academy of Sciences (Shanghai, China) and cultured in Keratinocyte complete medium(C120JV; BasalMedia, Shanghai, China). The LNCaP_AI cell line was established by culturing LNCaP cells in RPMI-1640 medium with 10% (w/v) charcoal-stripped FBS (CS-FBS) for > 6 months. All cells were maintained at 37℃ with 5% (v/v) CO2. Culture media were changed every 2–3 days depending on cell status and density.
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Cell Culture and Transfection Techniques

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HEK293, HEK293T, MCF-7, and HCT116 cells were originally obtained from ATCC and grown at 37 °C in 5% CO2 humified chambers in DMEM (D6429, Sigma) supplemented with 10% fetal bovine serum (FBS; F7524, Sigma) and penicillin/streptomycin. Cells were authenticated through STR (Short Tandem Repeat) profiling and mycoplasma tested by Microsynth (Switzerland). Exponentially growing HEK293 cells were plated at a consistent confluence and transfected with plasmids using Fugene 6 (E2692, Promega) according to the manufacturer’s instructions as described45 (link), 60 (link). 1.2 × 10 E6 of HCT116 cells were transiently transfected with 1.0 μg pcDNA3-based plasmids using the nucleofector kit V (VCA-1003, Lonza) as defined by the manufacturer. Drosophila S2R + cells were maintained at 24 °C in Schneider’s Drosophila Medium (217200024, Invitrogen) supplemented with heat inactivated FBS (10082147, Invitrogen) and penicillin/streptomycin. S2R + cells were transiently transfected with pAW-based plasmids using Effectene (301425, Qiagen) according to the manufacturer’s instructions.
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Cell Culture and Transfection of HeLa and HepG2 Cells

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The human cervix epithelial adenocarcinoma cell line HeLa was purchased from the American Type Culture Collection, and the liver carcinoma cell line HepG2 from the European Collection of Authenticated Cell Cultures (Sigma-Aldrich Chemie N.V., Zwijndrecht, the Netherlands). General cell culture supplies were from Gibco (Life Technologies Europe B.V., Bleiswijk, the Netherlands) if not indicated otherwise: HeLa cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) + 4.5 g/l d-glucose + l-glutamine + 25 mm HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) without pyruvate (42430-025) to which MEM nonessential amino acids (11140-035) were added and 10% fetal bovine serum (Sigma, F7524, Sigma-Aldrich Chemie N.V). HepG2 cells were cultured in Eagle's Minimum Essential Medium (EMEM) + Earle’s salts without l-glutamine (21090-022) to which MEM nonessential amino acids (11140-035) were added and 10% fetal bovine serum (American Type Culture Collection, ATCC 30-2020, LGC Standards GmbH, Wesel, Germany).
For transfections, HeLa and HepG2 cells were seeded at approximately 80% density in 96-well plates (Greiner Bio-One 655180). HeLa cells were transfected using the TransIT-HeLaMONSTER Transfection Kit (MIR 2904) and HepG2 cells with TransIT-LT1 Transfection Reagent (MIR 2304) applying the standard protocols (both from Mirus Bio LLC, Sopachem B.V., Ochten, the Netherlands).
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