Rpmi 1640 medium

After the successful isolation of the CD14⁺ monocytes, the cells were counted and seeded in a density of 2 × 10⁶ cells/ml, either in a 10 cm² plates (of about 20 × 10⁶ cells) (Thermo scientific) in order to perform ChIP experiments or in 6-well plates (of about 4 × 10⁶ cells/well) (Thermo scientific) to extract RNA. For culturing and differentiation of monocytes to macrophages RPMI 1640 medium (VWR) was supplemented with 10 % human serum {off the clot, type AB (A&E Scientific, PAA, Pasching, Austria, lot number: C02108-1021)}, 0.1 mg/ml streptomycin (Invitrogen, Life Technologies), 100 U/ml penicillin (Invitrogen, Life Technologies) and 0.1 mM L-glutamine (Invitrogen, Life Technologies). The cells were kept at 37 °C under a 5 % CO2 atm. The medium was changed, during the differentiation process of monocytes to macrophages, 4 and 7 days after seeding. For the RNA extraction and the subsequent array analysis, the cells were extracted 2 days, 4 days, 7 days and 11 days after seeding (see Fig. 2). In order to perform ChIP experiments the chromatin of day 11 cells was cross-linked (see Fig. 2).

The JIMT-1 human breast carcinoma cell line (ACC589) was purchased from the German Collection of Microorganisms and Cell Cultures (Braunschweig, Germany). The normal-like breast epithelial MCF-10A cell line (CRL-10317), the cancer cell lines MCF-7 (HTB-22) and HCC1937 (CRL-2336) were purchased from American Type Culture Collection (Manassas, VA, USA). The cells were tested negative for mycoplasma (Eurofins, Konstanz, Germany).
The JIMT-1 cells were routinely cultured at 37 °C in a humidified incubator with 5% CO₂ in air. The cells were cultured in DMEM/Ham’s F-12 medium supplemented with 10% fetal bovine serum (FBS), glutamine (2 mM), non-essential amino acids (1 mM), insulin (10 μg/ml), penicillin (100 U/ml), and streptomycin (100 μg/ml).
MCF-10A, MCF-7, and HCC1937 cell lines were cultured in RPMI 1640 medium (VWR) supplemented with 10% heat-inactivated FBS (VWR, Lund, Sweden), glutamine (2 mM), 1 mM non-essential amino acids (VWR), 10 μg/ml insulin (Sigma-Aldrich, Stockholm, Sweden), and 100 U/ml penicillin/100 μg/ml streptomycin (VWR). The MCF-10A cells were also supplemented with 20 ng/ml epidermal growth factor (Sigma-Aldrich), 50 ng/ml cholera toxin (Sigma-Aldrich), and 250 ng/ml hydrocortisol (Sigma-Aldrich). Finally, the HCC1937 medium was supplemented with 20 ng/ml epidermal growth factor (Sigma-Aldrich) besides the mentioned supplements.

HepG2 and Huh7 cells were obtained from ATCC. MDA-MB231 cells were obtained from Dr. Hasan Korkaya who originally purchased from ATCC. All cell lines were maintained in DMEM medium supplemented with 10% FBS (VWR). The Epstein-Barr virus (EBV)–transformed B-lymphoblastoid cell lines (B-LCL) used for alloreactivity test were obtained from either Sigma or Fred Hutchinson Cancer Research Center, and maintained in RPMI 1640 medium supplemented with 15% FBS (VWR). Primary adult human hepatocytes were obtained from Lonza. Primary human lung and kidney epithelial cells were purchased from Novabiosis and Lifeline, respectively. Induced pluripotent stem cell-derived iCell® Neurons, Astrocytes, Cardiomyocytes and Endothelial Cells were all from FUJIFILM Cellular Dynamics, Inc. The culture medium, supplements and plate coating reagents for each cell type were purchased from vendors as designated by the cell suppliers. Primary hepatocytes and the four iCells were originally from HLA-A^*02:01⁺ donors, according to vendor-provided information. Primary lung and kidney epithelial cells were originally from HLA-A2⁺ donors, in-house PCR (25 (link)) and sequencing further confirmed they also carry HLA-A^*02:01 allele.