Table 3.
Key resources table.
| Reagent of resource | Source | Identifier | Notes |
|---|---|---|---|
| ANTIBODIES | |||
| Anti-CD117 (cKIT) | Biolegend | 313201 | |
| Anti-AXL (10c9) | BerGenBio, Bergen, Norway | N/A | |
| Cytokeratin 14 antibody | Thermo scientific | PA5-16722 | |
| Anti-Cytokeratin 19 | Abcam | AB7754 | |
| Anti-Collagen type IV | Merck millipore | MAB3326 | |
| Anti-Collagen I | Abcam | AB34710 | |
| Anti-Laminin-5 | Merck millipore | MAB19562 | |
| Anti-Laminin | Sigma-aldrich | L9393 | |
| Anti-human CD326 (EPCAM) | Biolegend | 34202 | |
| Anti-AXL (mAb: 1H12) | BerGenBio, Bergen, Norway | N/A | |
| Anti-COL6A3 | Novus biologicals | NBP-71566 | |
| BIOLOGICAL SAMPLES | |||
| The human FFPE-healthy mammary gland and breast cancer tissues | The Department of Pathology, Haukeland University Hospital, Bergen, Norway, and the University Hospital of Iasi, Iasi, Romania | N/A | |
| Chemicals, peptides, and recombinant proteins | Concentration in MEMA, Reference; relevance in cancer | ||
| Bone morphogenetic protein 2/7 heterodimer (BMP-2/7) | R&D systems | 3229-BM/CF | 1 μg/ml, (Ye et al., 2009) |
| Bone morphogenetic protein 4 (BMP-4) | R&D systems | 113-BP/CF | 1 μg/ml, (Ye et al., 2009) |
| Carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) | R&D systems | 3934-CM-050 | 1 μg/ml, (Beauchemin and Arabzadeh, 2013) |
| Carcinoembryonic antigen-related cell adhesion molecule 8 (CEACAM8) | Abnova | H00001088-P01 | 1 μg/ml, (Beauchemin and Arabzadeh, 2013) |
| CD44 | R&D systems | 3660-cd | 1 μg/ml, (Karousou et al., 2014) |
| Collagen I (COL1) | Sigma-Aldrich | C8919 | 100 μg/ml, (Insua-Rodriguez and Oskarsson, 2016) |
| Collagen IV (COL4) | Sigma-Aldrich | C5533 | 100 μg/ml, (Insua-Rodriguez and Oskarsson, 2016) |
| CollagenXXIIIA1 (COL23A1) | R&D systems | 4165-CL | 1 μg/ml, (Spivey et al., 2012) |
| CollagenVIα3 (COL6A3) | MyBiosource | MBS958856 | 1 μg/ml, (Karousou et al., 2014) |
| E-Cadherin (ECAD) | Sigma-Aldrich | E2278 | 1 μg/ml, (Yu and Elble, 2016) |
| Epidermal growth factor (EGF) | Sigma-Aldrich | E9644 | 1 μg/ml, (Voudouri et al., 2015) |
| Fibroblast growth factor basic (FGF-2) | R&D systems | 233-FB-025 | 1 μg/ml, (Zheng et al., 2014) |
| Fibronectin (FN1) | Sigma-Aldrich | f2518 | 100 μg/ml, (Insua-Rodriguez and Oskarsson, 2016) |
| Growth arrest specific 6 (GAS-6) | R&D systems | 885-GS-050 | 1 μg/ml, (Mc Cormack et al., 2008) |
| Hepatocyte growth factor (HGF) | R&D systems | 294-HG-005 | 1 μg/ml, (Ho-Yen et al., 2015) |
| Hyaluronan HMW (HA) | R&D systems | GLR002 | 100 μg/ml, (Karousou et al., 2014) |
| Insulin like growth factor-1 (IGF1) | R&D systems | 291-Gi-250 | 1 μg/ml, (Voudouri et al., 2015) |
| Interferon- γ (IFN-γ) | Gibco | PHC4031 | 1 μg/ml, (Esquivel-Velazquez et al., 2015) |
| Interleucin-1β (IL-1β) | Biolegend | 579404 | 1 μg/ml, (Esquivel-Velazquez et al., 2015) |
| Interleucin-6 (IL-6) | Biolegend | 570804 | 1 μg/ml, (Esquivel-Velazquez et al., 2015) |
| Interleucin-8 (IL-8, CXCL8) | Biolegend | 574204 | 1 μg/ml, (Palacios-Arreola et al., 2014) |
| Laminin-111 (LAM1) | Sigma-Aldrich | I2020 | 80 / 100 μg/ml, (Insua-Rodriguez and Oskarsson, 2016) |
| Laminin-332 (LAM5) | Abcam | ab42326 | 20 μg/ml, (Insua-Rodriguez and Oskarsson, 2016) |
| Leptin | Sigma-Aldrich | L4146 | 1 μg/ml, (Garcia-Robles et al., 2013) |
| Lumican | Sigma-Aldrich | 2846 | 1 μg/ml, (Nikitovic et al., 2014) |
| Melanoma growth stimulating activity alpha (GRO-α/CXCL1) | Sigma-Aldrich | G0657 | 1 μg/ml, (Palacios-Arreola et al., 2014) |
| Nidogen1 | R&D systems | 2570-nd | 1 μg/ml, (Insua-Rodriguez and Oskarsson, 2016) |
| Osteopontin (OPN) | Novus Biologicals | NBC1-21056 | 1 μg/ml, (Insua-Rodriguez and Oskarsson, 2016) |
| Osteoprotegerin (OPG) | R&D systems | 185-OS-025 | 1 μg/ml, (Weichhaus et al., 2015) |
| Stem cell factor (SCF) | R&D systems | 255-SC-010 | 1 μg/ml, (Mimeault et al., 2007) |
| Stromal derived factor-1 (SDF-1β/CXCL12) | Abnova | P4470 | 1 μg/ml, (Palacios-Arreola et al., 2014) |
| Tenascin C (TNC) | Chemicon | CC065 | 1 μg/ml, (Insua-Rodriguez and Oskarsson, 2016) |
| Tumor growth factor β (TGFβ) | Biolegend | 580704 | 1 μg/ml, (Esquivel-Velazquez et al., 2015) |
| Paclitaxel | Sigma-Aldrich | T7191 | |
| rat tail Collagen type I | Ibidi | 50201 | |
| Collagen type 1, calf skin | Sigma-Aldrich | C8919 | |
| Matrigel, growth factor reduced | Corning | 356231 | |
| CRITICAL COMMERCIAL ASSAYS | |||
| RT2Profiler™ PCR arrays, human stem cell | Qiagen | PAHS-405ZF | |
| RT2Profiler™ PCR arrays, human epithelial to mesenchymal transition (EMT) | Qiagen | PAHS-090ZF | |
| Click-iT® Plus Edu imaging kit | Molecular probes | C10337 | |
| RT2 SYBR Green PCR Master Mix | Qiagen | 330503 | |
| RT2-First Strand Kit | Qiagen | 330401 | |
| Quick-RNA MicroPrep | Zymo Research | R1050 | |
| CellTiter-Glo 2.0 Assay | Promega | G9242 | |
| EXPERIMENTAL MODELS: CELL LINES | |||
| HMEC progression series | Dr. Martha Stampfer, Lawrence Berkeley national Laboratory, CA, USA | 184 | |
| OLIGONUCLEOTIDES | |||
| RNAScope probe for AXL | Advanced cell diagnostics | Probe-Hs-AXL-C2 | |
| RNAScope probe for IL-8 | Advanced cell diagnostics | Probe-Hs-IL8-C1 | |
| RNAScope probe for OPN | Advanced cell diagnostics | Probe-Hs-SPP1-C1 | |
| SOFTWARE AND ALGORITHMS | |||
| Cell profiler | www.cellprofiler.org | ||
| R-language, R-studio | www.R-project.org/ | ||
| Cytobank | cellmass.cytobank.org | ||
| IC50 toolkit | www.ic50.tk | ||