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110 protocols using d5796

1

Cell Culture Protocols for Tumor Cell Lines

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CMT 167 cells (kind gift from Prof. Paola Allavena, Humanitas Research Hospital) were cultured in Gibco Dulbecco's Modified Eagle Medium (DMEM), high glucose (Sigma‐Aldrich, #D5796), with 10% Fetal Bovine Serum (FBS, Sigma‐Aldrich #F7524), 2 mM L‐glutamine and 100 U/mL penicillin–streptomycin (Pen/strep). 4T1 cells (CRL‐2539, American Type Culture Collection (ATCC)) were grown in RPMI 1640 Medium with 10% FBS and 100 U/mL Pen/strep. KPCY cells (2838c3, Kerafast) were cultured in DMEM (Sigma‐Aldrich #D5796) with 10% FBS and 100 U/mL Pen/strep. MC38 cells (ENH204, Kerafast) were cultured in low glucose DMEM (Sigma‐Aldrich #D6046) with 10% FBS, 2 mM L‐ glutamine, 1* non‐essential amino acids, 1 mM sodium pyruvate, 10 mM HEPES (4‐(2‐hydroxyethyl)‐1‐piperazineethanesulfonic acid), and 100 U/mL Pen/strep. All chemicals were from Sigma‐Aldrich unless specified. Cells were thawed and maintained in exponential growth for 2–3 weeks at 37°C and 5% CO2 before implantation.
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2

Cell Culture Conditions for Murine and Human Fibroblasts

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Wild type (Wt) and XPG-depleted (Xpg-/-) murine embryonic fibroblasts (MEFs) [23 (link)] were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma, D5796), supplemented with 1% penicillin/streptomycin (Gibco, 11548876) and 20% heat-inactivated fetal bovine serum (Corning, 35-015-CV). MRC5-SV, XPCS1RO-SV [24 (link)], GM14930-SV (Coriell, GM14930) and GM14931-SV (Coriell, GM14931) were grown in DMEM (Sigma, D5796), supplemented with 1% penicillin/streptomycin (Gibco, 11548876) and 10% non-heat-inactivated fetal bovine serum (Corning, 35-015-CV).). All these cell lines were grown at 37°C with 5% CO2 and 3% O2 to reduce oxidative damage. XPCS1RO-SV+XPG-GFP [25 (link)] were grown with 200 μg/mL of G418 (Sigma Aldrich, G8168-50ML). They were grown at 37°C with 5% CO2.
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3

Glioma and Neural Progenitor Cell Cultures

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TS603, TS667, TS543 were obtained from Memorial Sloan Kettering Cancer Center (MSKCC). SU-AO3, NCH612 glioma lines were described previously [23 (link)]. The patient-derived IDH1-mutant glioma lines were routinely subjected to panel sequencing analysis [26 (link)] and immunoblotting to confirm the expression of mutant IDH1 (R132H). Glioma lines were maintained as neurospheres in NeuroCult (StemCell Technologies) with 2 µg/ml heparin sulfate (Sigma), 20 ng/ml of EGF (StemCell Technologies), and FGF2 (StemCell Technologies). PC12 cells (provided by Dr. Agarwal, Heidelberg University; Dr. Chang, Gachon University) were maintained in DMEM (D5796, Sigma) supplemented with 10% horse serum (H1138, Sigma) and 1% penicillin–streptomycin. Human neural progenitor cells (SCC008, Sigma) were maintained in DMEM (D5796, Sigma) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin–streptomycin. All cells were grown in a 5% CO2 humidified incubator at 37 °C.
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4

Internalization of MSC-EVs by Endothelial Cells

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MCEC cells were seeded on glass bottom dishes (Ø 35 mm, WillCo Wells B.V.) at a density of 5 × 104 cells/dish in complete DMEM medium (#D5796, Merck) supplemented with 5% FBS (#F2442, Merck). After 24 h post seeding, cells were washed with PBS (w/o Ca2+, Mg2+, HyClone) and divided into two groups:

Control—further culture of MCECs in complete DMEM medium with 5% FBS for the following 24 h;

Microenvironment mimicking inflammation and hypoxia—further culture of MCECs in complete DMEM medium with 1% FBS, 10 ng/mL IL-1β (#211-11B, Peprotech) and 10 ng/mL TNF-α (#315-01, Peprotech) for the following 24 h.

Fluorescently-labelled MSC-EVs (50 µg) were then added into each dish and MCECs were further incubated at 37 °C in humidified atmosphere containing 5% CO2 and 21% O2 (Control) or 5% CO2 and 2% O2 (microenvironment of inflammation and hypoxia). Internalization of MSC-EVs by MCEC cells was examined after 2, 4 and 24 h of incubation with EVs by using Leica DMI6000B inverted fluorescence microscope (ver. AF7000, Leica Microsystems) equipped with Leica Application Suite X software (Leica Microsystems). The mean fluorescence intensity of MCECs was measured using ImageJ software (Maryland, USA).
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5

Cell Proliferation and Differentiation

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DMEM (Merck #D5796) containing 10% fetal calf serum (Sigma Aldrich #F7524-500ML) and 1% Penicilin-Streptamycin-Glutamine (PSG) was used to keep cells in proliferation. Transient transfections of cell were always performed using Lipofectamine 3000 (ThermoFisher #L3000075) according to the manufacturer’s protocol for 24 h or 48 h. For differentiation of C2-cells DMEM containing 2% HS and 1% PSG was used.
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6

Cell Culture and BH3 Mimetics Protocol

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U87 glioblastoma cells were purchased from the ATCC (Manassas, Virginia, USA) and cultivated in Dulbecco's modified Eagle's high glucose medium (DMEM, D5796, Merck, Darmstadt, Germany) supplemented with 10% FBS (D7524, Merck), 1% non-essential amino acids and 1% antibiotics (penicillinstreptomycin, P4333, Merck). Mantle cell lymphoma (MCL) cell line HBL-2 was obtained from Prof. Pavel Klener (HBL-2 cells were originally obtained from Prof. Martin Dreyling, Munich, Germany), and cultivated in Iscove's Modified Dulbecco's Medium media (IMDM, I7633, Merck) supplemented with 15% FBS (F7524, Merck) and 1% antibiotics (Penicillin-Streptomycin, P4333, Merck). Cultured cells were regularly tested for mycoplasma infection using the MycoAlert™ kit (LT07-318, Lonza, Basel, Switzerland), and only mycoplasma-negative cells were used. BH3 mimetics were purchased from MedChemExpress (Monmouth Junction, New Jersey, USA) and, unless stated otherwise, all other chemicals were from Merck. HCT-116 Bax/Bak -/-cells were kindly provided by Richard Youle (National Institutes of Health, Bethesda, Maryland, USA).
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7

Culture of Human Liver Stem Cells

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The human LX-2 HSC line (SCC064, MERCK) was grown in Dulbecco’s Modified Eagle’s Medium (DMEM) high glucose (D5796, MERCK) supplemented with 2% (v/v) FBS and 1% (v/v) Glutamine-Penicillin-Streptomycin solution.21 (link)
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8

Primary Neuron Culture from Mouse Cortex

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Embryonic C57BL/6J mice (15.5-16.5 days old) were used for primary neuron culture. The frontal cortices and hippocampi were dissected from the brains in cold HEPES-buffered, calcium and magnesium-free Hank's balanced salt solution (HBSS; 14175-103, Thermo Fisher Scientific, Waltham, MA, USA) and dissociated in HBSS containing 0.25% papain (LS003127, Worthington Biochemical Corporation, Lakewood, NJ, USA), 0.1% L-cysteine (C7352, Merck, Darmstadt, Germany), 0.1% bovine serum albumin (BSA; A2153, Merck), and 0.01% DNase I (D4263, Merck) at 37°C for 12 minutes. The enzymatic digestion was stopped by adding a plating medium (Dulbecco's modified Eagle medium, D5796, Merck, containing 10% fetal bovine serum). Tissues were dissociated by pipetting, centrifuged at room temperature for 10 minutes, and resuspended in the plating medium. Cells were counted, seeded at a density of 25,000 cells/cm 2 on culture plates or glass coverslips previously coated with 0.01% poly-L-lysine (P8920, Merck), and incubated at 37°C. After 2 hours, the plating medium was replaced by a culture medium (Neurobasal™ medium
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9

GFP-Tagged BoHV-1 Infection in MDBK Cells

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Wild type Madin-Darby bovine kidney cells (MDBK), Cas9+/+ MDBK cells or dCas9+/+ cells [49 (link)] were cultured in DMEM (D5796, Sigma, Tokyo, Japan) supplemented with 5% horse serum (26050088, Gibco), 1% Pen/Strep (15140122, Gibco), 1% L-glutamine (25030024, Gibco), 1% NEAA (11140035, Gibco, Paisley, Scotland), and 1% sodium pyruvate (11360039, Gibco). Cells were kept in an incubator set at 37 °C with 5% CO2. A GFP tagged BoHV-1 strain based on strain Jura [53 (link)] was used throughout the experiment. The GFP protein is fused to the VP26, a minor capsid protein of BoHV-1.
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10

FANCD2 and UHRF1 Localization Dynamics

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HeLa cells (female) were grown in DMEM (D5796, Sigma) supplemented with 10% FBS. EGFP-fused FANCD2 and mCherry-fused UHRF1 cDNA were expressed using a derivative of the pOZ-N plasmid and sorted using α-IL2R coupled magnetic beads (Dynabeads goat anti-mouse IgG) as described in (Nakatani and Ogryzko, 2003 (link)). Transfections of plasmid DNA were carried out using FuGENE6 (Promega) according to the manufacturer’s instructions.
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