Additional file 3 of Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia

Additional file 3. Supplementary methods. 1. ChIA-PET data processing and clustering of interaction PETs. 2. Comparison of ChIA-PET data for calling of binding peaks, loops, and chromatin domains. 3. Identification and classification of RARα and PML-RARα binding sites. 4. Identification and characterization of PML-RARα-mediated chromatin interactions. 5. Visualization of 2D contact map and BASIC browser. 6. 3D chromatin structure modeling, measurement of 3D structure condensation and visualization. 7. Identification of binding motifs at PML-RARα peak regions. 8. Comparison of RNAPII-mediated chromatin interactions between control and treatment condition. 9. RNA-Seq and differential gene expression analysis. 10. ChIP-Seq analysis. 11. Identification and characterization of super-enhancers. 12. Quantification and statistical analysis methods.