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Additional Supporting Information may be found in the online version of this article.

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sc-12-0914_sm_SupplFigure1.pdf866KSupplementary Figure 1: FoxG1 and Bmi1 knockdown lead to an efficient reduction in their transcript and protein levels. shRNA-mediated knockdown of (a) FoxG1 revealed a significant knockdown in shFoxG1-2 construct when compared to cells transduced with a control shRNA construct (n=3, P=0.0047). All other constructs, shFoxG1-1, shFoxG1-3, shFoxG1-4 had varying levels of knockdown but were not significant at transcript level (n=3, P=0.5669, n=3, P=0.2636 and n=3, P=0.1425, respectively). (b) shRNA-mediated knockdown of (b) Bmi1 revealed a significant knockdown in shBmi1-3 construct when compared to cells transduced with a control shRNA construct (n=3, P=0.001). All other constructs, shBmi1-1 and shBmi1-2, had varying levels of knockdown but were not significant at transcript level (n=3, P=0.7923, and n=3, P=0.2064, respectively). (c) Overexpression construct for FoxG1 revealed a significant increase in FoxG1 expression compared to cells transduced with a control construct (n=3, P=0.0018). **P<0.05, ***P<0.005
sc-12-0914_sm_SupplFigure2.pdf1474KSupplementary Figure 2: Functional characterization of FoxG1 knockdown/overexpression and Bmi1 knockdown constructs through in vitro limiting dilution assays. Characterization of (a) 4 shFoxG1 and (b) 3 shBmi1 constructs with (c) shFoxG1-2 and shBmi1-3 showing the greatest reduction in sphereforming capacity. (d) Cells transduced with OE FoxG1 and OE FoxG1+shBmi1 constructs displayed an increase and decrease in sphere-forming capacity, respectively.
sc-12-0914_sm_SupplFigure3.pdf1231KSupplementary Figure 3: Representative flow cytometric cell sorting plot for CD15 in Daoy and Med8a medulloblastoma stem cells. (a) Flow plot showing side scatter against forward scatter for Daoy MB stem cells. (b) Flow plot of sort sample showing 5.16% of cells being CD15+. (c) Flow plot showing side scatter against forward scatter for Med8a MB stem cells. (d) Flow plot of sort sample showing 43.29% of cells being CD15+.
sc-12-0914_sm_SupplFigure4.pdf1387KSupplementary Figure 4: FoxG1 and Bmi1 are differentially enriched in Med8a medulloblastoma cells. (a) FoxG1 (n=3, P=0.00044) and (b) Bmi1 (n=3, P=0.0031) expression are significantly elevated in Med8a MB cells grown in NSC conditions compared to normal human NSCs (n=3). (c) FoxG1 is specifically enriched in CD15+ Med8a MB stem cells compared to CD15- cells (n=5, P=0.00041), however, (d) no difference is observed in Bmi1 expression between CD15+ and CD15- cells (n=5, P=0.7332). (e) Flow plot (left) showing side scatter against forward scatter for Med8a MB stem cells along with (right) FoxG1 and Bmi1 levels showing 99.39% positivity for FoxG1 and 3.12% positivity for Bmi1. **P<0.005, ***P<0.0005
sc-12-0914_sm_SupplFigure5.pdf1005KSupplementary Figure 5: FoxG1 regulation of MB BTIC differentiation. A general trend demonstrating a (a) decrease in GFAP, MAP2, and OLIG2 expression was observed in OE FoxG1 cells compared to control cells (n=3), whereas an (b) increase in neural differentiation marker expression was observed in shFoxG1 cells when compared to control cells (n=3). (c) Additionally, FoxG1 expression was found to decrease with differentiation in primary human MB BTICs (n=3, P=0.0482). *P<0.05
sc-12-0914_sm_SupplFigure6.pdf2080KSupplementary Figure 6: Putative MB BTIC marker, CD15, is preferentially expressed in subgroup 3 and 4 MBs. Representative images of differential cytoplasmic CD15 expression in (a) Wnt, (b) Shh, (c) Group 3, and (d) Group 4 MBs. (e) Graphical representation of low/no cytoplasmic CD15 staining to high cytoplasmic positivity within MB subgroups. CD15 staining is marked in non-Shh/Wnt subgroups. (Magnification: ×200)
sc-12-0914_sm_SupplTable1.pdf13KSupplementary Table 1: Candidate gene list
sc-12-0914_sm_SupplTable2.pdf12KSupplementary Table 2: Statistical evaluation of candidate genes
sc-12-0914_sm_SupplTable3.pdf7KSupplementary Table 3: Medulloblastoma stem cell patient isolates: Clinicopathological data
sc-12-0914_sm_SupplTable4.pdf8KSupplementary Table 4: qRT-PCR & ChIP primers

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