Promoter shape varies across populations and impacts promoter evolution and expression noise

All coordinates are relative to the dm3 assembly

We provide the Supplementary Tables and convenient media produced for Schor et al. 2017. Please refer to our Supplementary Tables description material [ / ] Importantly, the Furlong lab hosts an interactive HTML table containing relevant plots and information about all significant associations found with the joint model. Detailed information for each region is accessible by clicking on the relevant location hyperlink in the Window column. (Access the detailed description of the table). Additionally, we provide tables (tab-delimited files) for each window with the raw p-values for all variants. We included all windows with a significant association for the multi-trait 3PC (all time-points together, first 3 principal components as phenotype), i.e. all those included in Supplementary Table 2. We provide two compressed files, which contain all tables:

1. 3PC: p-values resulting from the multi-trait 3PC model (all time-points together, first 3 principal components as phenotype)
2. Mean: p-values resulting from the multi-trait Mean model for the same windows as with the 3PC model (all time-points together, mean CAGE signal as phenotype)

Both tables contain, besides chromosome and position of all tested variants, the p values for the common effect and the time-specific terms. Supplementary Tables:

• Supplementary Table 1: Promoter regions used for tssQTL calling (GFF3 file containing the 1024bp windows used to call the tssQTL)
• Supplementary Table 2: Summary of all significant associations found with the joint model (tab-delimited text file). This table is the same than our HTML table but in a tab-delimited text format.
• Supplementary Table 3: Summary of high-confidence associations found with the joint model (tab-delimited text file). This table contains the same windows as Supplementary Table 2, with exception of those QTL labeled as internal or enzyme artifact.
• Supplementary Table 4: Core promoter motifs obtained de novo (tab-delimited text file). The file contains the motifs found, grouped in similarity clusters and with those having IC < 8 filtered out.
• Supplementary Table 7: CAGE TSS clusters (GFF3 file containing the cage peaks or TSS clusters)

Raw data is available at ArrayExpress:

• Accession E-MTAB-4787 — 5′ CAGE at three embryonic time points in 81 Drosophila lines