A limiting-dilution assay was performed on the TOP-GFPlow, TOP-GFPhigh, or TOP-GFPwhole populations of the three indicated TOP-GFP cultures. Cells were left untreated, or treated with 25 ng/ml HGF, 1:2 dilution of MFCM, or 500 nM PHA-665752 (PHA), as indicated. The bar graphs present the clonogenic potential of each culture with error bars representing 95% confidence intervals (y-axis is log2 scale). This experiment was performed once for each culture. See Materials and methods and Registered Report (Evans et al., 2015) for details on limiting-dilution statistics and scheme. Planned contrast between TOP-GFPlow vs TOP-GFPhigh: E450 (χ2 = 39.8, uncorrected p=2.82×10−10, corrected p=1.69×10−9); CSC1 (χ2 = 4.82, uncorrected p=0.028, corrected p=0.169); Co100 (χ2 = 7.59, uncorrected p=0.0059, corrected p=0.035). Planned contrast between TOP-GFPlow vs TOP-GFPlow + HGF: E450 (χ2 = 1.49, uncorrected p=0.223, corrected p>0.99); CSC1 (χ2 = 0.337, uncorrected p=0.562, corrected p=0.99); Co100 (χ2 = 12.7, uncorrected p=3.70×10−4, corrected p=0.0022). Planned contrast between TOP-GFPlow vs TOP-GFPlow + MFCM: E450 (χ2 = 1.96, uncorrected p=0.162, corrected p=0.969); CSC1 (χ2 = 4.18, uncorrected p=0.041, corrected p=0.245); Co100 (χ2 = 28.7, uncorrected p=8.26×10−8, corrected p=4.96×10−7). Planned contrast between TOP-GFPlow + HGF vs TOP-GFPlow + HGF + PHA: E450 (χ2 = 0.376, uncorrected p=0.540, corrected p>0.99); CSC1 (χ2 = 34.0, uncorrected p=5.64×10−9, corrected p=3.39×10−8); Co100 (χ2 = 5.13, uncorrected p=0.024, corrected p=0.141). Planned contrast between TOP-GFPlow + MFCM vs TOP-GFPlow + MFCM + PHA: E450 (χ2 = 61.0, uncorrected p=5.71×10−15, corrected p=3.43×10−14); CSC1 (χ2 = 43.5, uncorrected p=4.14×10−11, corrected p=2.48×10−10); Co100 (χ2 = 17.6, uncorrected p=2.67×10−5, corrected p=1.60×10−4). Planned contrast between TOP-GFPwhole vs TOP-GFPwhole + PHA: E450 (χ2 = 68.3, uncorrected p=1.43×10−16, corrected p=8.56×10−16); CSC1 (χ2 = 72.2, uncorrected p=1.96×10−17, corrected p=1.17×10−16); Co100 (χ2 = 20.2, uncorrected p=6.91×10−6, corrected p=4.14×10−5). Additional details for this experiment can be found at https://osf.io/k9vce/.