Supplementary Materials

Supplementary Materials for:

Parallel Profiling of the Transcriptome, Cistrome, and Epigenome in the Cellular Response to Ionizing Radiation

Sharon Rashi-Elkeles, Hans-Jörg Warnatz, Ran Elkon, Ana Kupershtein, Yuliya Chobod, Arnon Paz, Vyacheslav Amstislavskiy, Marc Sultan, Hershel Safer, Wilfried Nietfeld, Hans Lehrach, Ron Shamir, Marie-Laure Yaspo, Yosef Shiloh*

*Corresponding author. E-mail: yossih{at}

This PDF file includes:

  • Fig. S1. IR-induced responses in CAL51 cells.
  • Fig. S2. p53-dependent transcriptional response to IR in CAL51 cells.
  • Fig. S3. Induction of noncoding RNAs by IR.
  • Fig. S4. ChIP-seq analysis for p53.
  • Fig. S5. Secondary transcription factors induced by IR.
  • Fig. S6. Responsiveness of p53 target genes to IR.
  • Fig. S7. ChIP-seq analysis for RelA.
  • Fig. S8. Relationship between gene expression and H3K4me3 abundance in promoters.
  • Fig. S9. Histone marks near IR-induced lncRNAs.
  • Fig. S10. Improved detection of weakly expressed genes by RNA-seq versus microarray.
  • Legends for tables S1 to S9
  • Table S10. Sequences of RT-PCR primers.

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Technical Details

Format: Adobe Acrobat PDF

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Early and late kinetics of IR-induced clusters (expression microarrays).
  • Table S2 (Microsoft Excel format). RNA-seq number of reads.
  • Table S3 (Microsoft Excel format). IR-responsive genes (RNA-seq).
  • Table S4 (Microsoft Excel format). GO analysis of the responsive genes.
  • Table S5 (Microsoft Excel format). RNA-seq expression matrix.
  • Table S6 (Microsoft Excel format). Microarray expression matrix.
  • Table S7 (Microsoft Excel format). IR-induced lncRNAs.
  • Table S8 (Microsoft Excel format). IR-induced p53-binding sites.
  • Table S9 (Microsoft Excel format). IR-induced RelA binding sites.

[Download Tables S1 to S2]

Citation: S. Rashi-Elkeles, H.-J. Warnatz, R. Elkon, A. Kupershtein, Y. Chobod, A. Paz, V. Amstislavskiy, M. Sultan, H. Safer, W. Nietfeld, H. Lehrach, R. Shamir, M.-L. Yaspo, Y. Shiloh, Parallel Profiling of the Transcriptome, Cistrome, and Epigenome in the Cellular Response to Ionizing Radiation. Sci. Signal. 7, ra42 (2014).

© 2014 American Association for the Advancement of Science