Supplementary Materials

Global mRNA polarization regulates translation efficiency in the intestinal epithelium

Andreas E. Moor, Matan Golan, Efi E. Massasa, Doron Lemze, Tomer Weizman, Rom Shenhav, Shaked Baydatch, Orel Mizrahi, Roni Winkler, Ofra Golani, Noam Stern-Ginossar, Shalev Itzkovitz

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Author contributions
  • Figs. S1 to S11
  • Captions for tables S1 to S7
  • References
Table S1
Sleuth output of differential gene expression analysis of laser capture microdissected apical and basal cell fragments in fasting mice. Columns: target_id: ensemble transcript id, ens_gene: ensemble gene id, ext_gene: gene symbol, b: sleuth apical bias, pval: sleuth Wald p-value, qval: FDR adjusted p-value, mean_obs: sleuth mean expression across all samples.
Table S2
Combined smFISH results and Sleuth output of differential gene expression analysis of fasting laser capture microdissected apical and basal cell fragments in mice of 14 genes. Columns: external_gene_name: gene symbol, median_fish: median of log2 transformed apical/basal ratios of smFISH quantification, lower_95CI: lower 95% confidence interval of median_fish, upper_95CI: upper 95% confidence interval of median_fish, rnaseq_apical_bias: sleuth apical bias, standard_error_of_rnaseq_bias: sleuth standard error of apical bias.
Table S3
Table of mass spectrometry results of laser-capture microdissected subcellular epithelial fragments. Columns: external_gene_name: gene ID that corresponds to the identified protein, median_normalized_protein_intensity_apical: median of sum normalized measured intensity across apical samples, median_normalized_protein_intensity_basal: median of sum normalized measured intensity across basal samples, apical_basal_ratio: apical/basal ratio of the two median intensity columns.
Table S4
Table of GSEA results of laser-capture microdissected subcellular epithelial fragments. Columns: Gene set: gene ontology gene sets, mRNA NES: GSEA normalized enrichment score of gene set in transcripts ranked according to apical bias (methods), mRNA FDRqval, mRNA NOMpval, protein NES: GSEA normalized enrichment score of gene set in proteins ranked according to apical bias (methods), protein FDRqval, protein NOMpval, type: classification of genes according to the combined patterns of mRNA and protein polarization - A=apical, B=basal, X=not significantly enriched, gene names: members of gene set.
Table S5
Table of translational efficiency and apical bias comparison of fasting and refed mice (Fig. 3A). Columns: target_id: ensemble transcript id, ens_gene: ensemble gene id, ext_gene: gene symbol, te_refed_vs_fasting: log2 transformed translational efficiency of refed mice minus log2 transformed translational efficiency of fasting mice, mean_te_fasting: mean of log2 transformed translational efficiency of fasting mice, mean_te_refed: mean of log2 transformed translational efficiency of refed mice, apical_bias_refed_vs_fasting: log2 20 transformed apical/basal tpm ratio of refed mice â€" log2 transformed apical/basal tpm ratio of fasting mice.
Table S6
Table of GSEA results of fasting versus refeeding mice. Columns: Gene set: gene ontology gene sets, mRNA NES fast: GSEA normalized enrichment score of gene set in transcripts of fasting mice ranked according to apical bias (methods), mRNA FDRqval fast, mRNA NOMpval fast, mRNA NES refed: GSEA normalized enrichment score of gene set in transcripts of refed mice ranked according to apical bias (methods), mRNA FDRqval refed, mRNA NOMpval refed, type: classification of genes according to the combined patterns of mRNA polarization in fasting and refeeding, A=apical, B=basal, X=not significantly enriched, TE change NES: GSEA normalized enrichment score of gene set in ranked TE differences (refed-fasting), TE change FDRqval, TE change NOMpval, gene names: members of gene set.
Table S7
Table of smFISH probe libraries used in this study.
Correction (20 September 2017): The reference list includes five additional citations: E. Lécuyer et al. (reference 4), S. Mili et al. (reference 5), H. Jambor et al. (reference 6), S. Nichterwitz et al. (reference 13), and R. Blecher-Gonen et al. (reference 30).
The original version is accessible here.