Additional file 1: of Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA

Supplementary Materials. Figure S1. The reproducibility of ChIP-seq peak shifts in a HeLa cell experiment. Figure S2. Shift between CTCF and cohesin bound sites in mouse cells. Figure S3. The boundaries of genomic regions covered by CTCF/cohesin. Figure S4. Shift between CTCF/cohesin proteins in human cell lines. Figure S5. Box plot representation of the strand specific shift between CTCF and cohesin proteins in human cell lines. Figure S6. Shift between CTCF/cohesin proteins in mouse cell and tissue types. Figure S7. Box plot representation of the strand specific shift between CTCF and cohesin proteins in mouse cell and tissue types. Figure S8. Distance distribution of cohesin proteins relative to the CTCF in human cell lines. Figure S9. Distance distribution of cohesin proteins relative to the CTCF in mouse cell and tissue types. Figure S10. DNA modeling. The model of the CTCF binding site (CTS) and a consensus prediction of 16964 aligned binding sites shows that the DNA double helix is not inherently curved in this region (inset), and that it is slightly less curved and more flexible than the surrounding regions. Figure S11. Mapping the shift values onto the B-DNA. Figure S12. Shift between interacting transcription factors (positive control). Figure S13. Lack of shift between interacting transcriptional regulator proteins (negative control). Table S3. Steps of ChIP-seq analysis pipeline. Table S4. Results of statistic analysis in case of two coherent samples. Table S5. Results of statistic analysis in case of more then two coherent samples. Table S6. Summary table of CTCF-cohesin samples. Table S7. Average values of CTCF/cohesin proteins related to CTS. Table S8. Median and Mean distance from CTCF summits. Table S9. Standard deviation of protein distances near CTSs. Table S10. Relative positions of the co-occupied transcription regulators used as controls. (DOCX 1860 kb)