2 and 3 and Supporting Information Fig. 4 and 7). In case of the 7AAD-based viability stain, the autofluorescence+ cells/debris were eliminated from the viable population due to their 7AAD/PE-Cy5.5-like autofluorescence properties. For intracellular anti-BrdU and Ki67 stainings the BrdU Flow Kit (BD Bioscience) was applied according to the manufacturer’s recommendations together with the 7AAD staining for the total cellular DNA content. The CD115 intracellular staining was performed with cells

fixed with 4% paraformaldehyde and permeabilized with 0.2% saponin in PBS. In the intracellular stainings, BAY 80-6946 datasheet viable cells are defined as scatter pregated to remove cellular debris. For the analysis of the level of marker expression, delta median fluorescence intensity (ΔMFI) was calculated according to the formula ΔMFI = MFI(Marker) − MFI(Isotype), where MFI(Marker) and MFI(Isotype) refer to the stainings of the same sample with the specific antibody and the isotype control antibody, respectively. The antibodies used are listed in Supporting Information Table 2. Flow cytometry analysis

was carried out with FACS Calibur and FACS Fortessa (BD Bioscience) devices and FlowJo Software (Tree Star, Ashland, OR). Preparation of whole cell lysates from tumor tissue and RNA extraction and cDNA synthesis from whole tumors, tumor cultures, and sorted cells were described elsewhere [41]. mRNA expression levels were analyzed either with a TaqMan or an Eva MK-8669 datasheet Green basing protocol as reported in [4]. The amplification of TATA-Box Binding Protein (TBP or Tbp) mRNA was used to normalize expression levels for both Casein kinase 1 methods. Expression

levels for the gene of interest are represented as the relative log2 amounts using the formula Egene = CtTbp − Ctgene. The sequences of primers with the corresponding amplification method are listed in Supporting Information Table 3. NT2.5 cells (provided by Dr. Elisabeth Jaffee), tumor, and BM single-cell suspensions were cultured in RPMI 1640 supplemented with 10% FCS, l-glutamine, 1 mM sodium pyruvate, 1 mM HEPES, 100 IU/mL penicillin, 100 μg/mL streptomycin, and 50 μg/mL gentamycin and 50 μM β-ME. Tumor cell culture conditioned medium was obtained from 24 h or 3 day cultures seeded at 1 × 106 cell/mL density and filtered with a 0.22 μm PES syringe filter to exclude any contamination with tumor cells. Levels of CSF1 in tumor cell culture conditioned media (24 h primary tumor culture) and whole cell tumor lysates (2-week-old tumors) were determined with the murine M-CSF standard ELISA development kit (Peprotech, Rocky Hill, NJ) according to the manufacturer’s protocol. The ChIP was performed essentially as described [42] with minor modifications. In brief, NT2.5 cells were grown to 80% confluence and stimulated for 30 min with 20 ng/mL IFN-γ (Peprotech) and/or 50 ng/mL TNF-α (Peprotech) or left untreated.