Supplemental materials for: Motakis et al
Files in this Data Supplement:
- Document 1. Supplemental methods, figures and table (PDF, 1.2 MB)
- Supplemental Table 2. Genes overexpressed by MCs (XLSX, 65 KB) - Genes with highest expression in at least one of the 9 MC samples and enrichment by at least 10-fold compared to the mean of all 893 FANTOM5 samples. Expression levels (in tpm) are given individually for each MC preparation, followed by the mean of the 3 MC subsets (ex vivo, expanded, expanded+stimulated) and of the mean of all MCs. The mean of all FANTOM5 samples and sample with next best expression are also given for comparison. The (putative) gene function is specified whenever information was available.
- Supplemental Table 3. Comparison between ex vivo and cultured MCs (XLSX, 3 MB) - Differentially expressed and non-differential genes of ex vivo and cultured MCs are given in separate worksheets (genes form the basis of Fig. 2A/B). Significantly differential promoters between the MC subsets are also specified.
- Supplemental Table 4. Comparison between resting and stimulated MCs (XLSX, 2.8 MB) - Differentially expressed and non-differential genes of expanded and expanded+stimulated MCs are given in separate worksheets (genes form the basis of Fig. 2C/D). Significantly differential promoters between the MC subsets are also specified.
- Supplemental Table 5. MC specific promoters and promoter versus gene expression analysis (XLSX, 144 KB) - Given are promoters with at least 50-fold higher activity in MCs than in non-MCs (FC=mean(MC)/mean(F5 w/o MC) >50). The fold change is likewise calculated for the level of the entire gene (i.e. all promoters combined). These two levels are compared to each other. At the top of the list are promoters with greatest selectivity in MCs if contrasted against their respective genes. At the bottom are those promoters for which full gene activity surpasses activity of the selected promoter (even though the promoter is still much more active in MCs than in non-MCs). Ex vivo MCs, expanded MCs, and expanded+stimulated MCs are given in separate worksheets. Basophils are also included for comparison.
- Supplemental Table 6. Genes with different promoter sets active in ex vivo as compared to cultured MCs (XLSX, 112 KB) - Given is a list of genes, for which the two MC subsets utilize a different set of promoters. No genes of this kind were detected for expanded versus expanded+stimulated MCs. The promoter swap for the gene EXOC6B is illustrated in Suppl. Figure 4.
- Supplemental Table 7. Motif activity in MCs (XLSX, 228 KB) - Motif activity was calculated by MARA (supplemental Methods) and is given for ex vivo, expanded, and expanded+stimulated MCs, as well as for basophils and non-MC blood samples (used for direct comparison). The motifs are ranked and sorted by "best motif ranking" for the ex vivo samples. Gene expression levels of the TFs binding to these motifs are also given for comparison.
- Supplemental Table 8. Comparison between basophils and MCs (XLSX, 2.6 MB) - Differentially expressed and non-differential genes of basophils and ex vivo MCs are given in separate worksheets (genes form the basis of Fig. 4C/D).