Supplementary Materials

Supplementary Materials for:

The Tumor Suppressor Ikaros Shapes the Repertoire of Notch Target Genes in T Cells

Anne-Solen Geimer Le Lay, Attila Oravecz, Jérôme Mastio, Claudia Jung, Patricia Marchal, Claudine Ebel, Doulaye Dembélé, Bernard Jost, Stéphanie Le Gras, Christelle Thibault, Tilman Borggrefe, Philippe Kastner,* Susan Chan*

*Corresponding author. E-mail: (P.K. and S.C.)

This PDF file includes:

  • Fig. S1. Characterization of T29 cells expressing dnMAML1-ER or Ik1-ER.
  • Fig. S2. Transcriptome analysis of Notch- and Ikaros-regulated genes in T29 cells.
  • Fig. S3. Comparison of ChIP-seq results with published data.
  • Fig. S4. Notch-dependent activation of 82 genes bound by RBPJ.
  • Fig. S5. Binding of RBPJ and ICN1 to Notch target genes.
  • Fig. S6. Conservation of the RBPJ-binding site downstream of the Myc gene.
  • Fig. S7. Notch target genes are frequently clustered near RBPJ peaks.
  • Fig. S8. Analysis of ICN1 ChIP-seq data.
  • Fig. S9. Input tracks for ChIP-seq data.
  • Fig. S10. Analysis of Ikaros binding to Hes1.
  • Fig. S11. Mutational analysis of Ikaros binding to the Lmcd1 L2 sequence.
  • Fig. S12. The binding of Ikaros and RBPJ to TGGGAA motifs that are present in coregulated target genes.
  • Fig. S13. Ikaros forms complexes with RBPJ in T cells.
  • Fig. S14. Global analysis of gene expression in Ikaros-deficient thymocytes.
  • Fig. S15. Dysregulation of Notch target genes in Ikaros-null DP thymocytes.
  • Fig. S16. Scheme of the floxed Ikzf1 allele.
  • Fig. S17. Analysis of ICN1 abundance and size in T-ALL cells from Ikf/f CD4-Cre+ mice.
  • Table S1. One hundred thirty-one genes activated by Notch and repressed by Ikaros.
  • Table S2. One hundred ten genes repressed by Notch and activated by Ikaros.
  • Table S3. Genomic RBPJ-binding regions and associated genes.
  • Table S4. ICN1-only peaks associated with genes repressed by Notch.
  • Table S5. Presence of RBPJ, ICN1, and Ikaros binding near the 131 genes coregulated by Ikaros and Notch.
  • Table S6. Putative Ikaros- and RBPJ-binding motifs associated with overlapping Ikaros/RBPJ peaks.

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Citation: A.-S. Geimer Le Lay, A. Oravecz, J. Mastio, C. Jung, P. Marchal, C. Ebel, D. Dembélé, B. Jost, S. Le Gras, C. Thibault, T. Borggrefe, P. Kastner, S. Chan, The Tumor Suppressor Ikaros Shapes the Repertoire of Notch Target Genes in T Cells. Sci. Signal. 7, ra28 (2014).

© 2014 American Association for the Advancement of Science