Supplementary Materials

Supplementary Materials for:

TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors

Zeinab Chitforoushzadeh, Zi Ye, Ziran Sheng, Silvia LaRue, Rebecca C. Fry, Douglas A. Lauffenburger, Kevin A. Janes*

*Corresponding author. Email: kjanes{at}virginia.edu

This PDF file includes:

  • Text S1. Detailed description of tensor PLSR.
  • Text S2. Detailed description of GATA6L mass spectrometry.
  • Fig. S1. Tensor PLSR modeling predicts overall transcript abundance but cannot link changes in transcript abundance to cytokine-induced signaling.
  • Fig. S2. Accuracy of tensor PLSR predictions.
  • Fig. S3. Induction of cluster #9 probe sets and repression by insulin.
  • Fig. S4. Disruption of NF-κB signaling does not widely affect the TNF-induced transcriptional response of cluster #9.
  • Fig. S5. Widespread TNF-insulin crosstalk among genes in transcriptional cluster #9.
  • Fig. S6. Immunolocalization of β-catenin is not altered by TNF stimulation or insulin costimulation in HT-29 cells.
  • Fig. S7. HT-29 cells lack GATA1, GATA4, and GATA5.
  • Fig. S8. Phylogeny of the human GATA family.
  • Fig. S9. Prolonged rapamycin treatment alters the proportion of GATA6S to GATA6L independently of TNF or insulin treatment.
  • Fig. S10. Insulin and CT99021 perturb GSK3 phosphorylation and activity.
  • Fig. S11. Phospho-GATA6L (Ser37) antiserum is specific for mobility-shifted wild-type GATA6L but not the S37A GATA6L mutant.
  • Fig. S12. GATA6L phosphorylation on Ser37 and GS phosphorylation on Ser641 are lost in a dose-dependent manner upon treatment with the GSK3 inhibitor CT99021.
  • Fig. S13. GATA6L occupies GATA binding sites in the promoters of genes within the crosstalk cluster.
  • Table S1. Top-scoring PEST sequences in the indicated proteins according to PEST-FIND.
  • Table S2. qRT-PCR primer sequences.
  • Table S3. ChIP primer sequences.
  • Legends for files S1 to S5
  • References (137140)

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Technical Details

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Other Supplementary Material for this manuscript includes the following:

  • File S1 (Microsoft Excel format). Microarray probe sets differentially altered with time or by stimulation with TNF, EGF, or insulin.
  • File S2 (Microsoft Excel format). Transcriptional clusters identified by CLICK.
  • File S3. Tensor PLSR model and associated files.
  • File S4 (Microsoft Excel format). Transcripts differentially altered by wild-type GATA6L overexpression with or without TNF stimulation.
  • File S5. Raw files and densitometric analysis of phospho-GATA6L (Ser37) immunoprecipitation and total GATA6 immunoblots.

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Citation: Z. Chitforoushzadeh, Z. Ye, Z. Sheng, S. LaRue, R. C. Fry, D. A. Lauffenburger, K. A. Janes, TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors. Sci. Signal. 9, ra59 (2016).

© 2016 American Association for the Advancement of Science