GO enrichment analysis for genes overlapping bins identified as differentially enriched via DiffBind (adjusted p value < 0.05) and overlapping a bin with a difference in PBS of > 0.9.

Two separate biological repeats, each containing siRNA knockdown of SENP3 and a non-targeting control in OE19, ChIPed using rabbit polyclonal antibody specific against SUMO2/3 antibody (Abcam), and sequenced separately. Differential binding analysis using DiffBind, very little difference between experiment and control found.

Additional file 2: Table S1. Differentially bound sites (DBSs) obtained from MCF7 cell line treated with 10nM E2 for 45 minutes in GSE94023 study. Table S2. Differentially bound sites (DBSs) obtained from MCF7 cell line treated with 10nM E2 for 45 minutes in GSE99626 study. Table S3. Differentially bound sites (DBSs) obtained from MCF7 cell line treated with 10nM E2 for 45 minutes in GSE67295 study. Table S4. Differentially bound sites (DBSs) obtained from MCF7 cell line treated with 10nM E2 for 45 minutes in GSE115607 study. Table S5. Differentially bound sites (DBSs) obtained from T47D cell line treated with 10nM E2 for 45 minutes in GSE80367 study. Table S6. Differentially bound sites (DBSs) obtained from T47D cell line treated with 100nM E2 for 45 minutes in GSE23893 study. Table S7. Differentially bound sites (DBSs) obtained from MCF7 cell line treated with 100nM E2 for 45 minutes in GSE23893 study. Table S8. Differentially bound sites (DBSs) obtained from MCF7 cell line treated with 100nM E2 for 45 minutes in GSE54855 study. Table S9. Differentially bound sites (DBSs) obtained from MCF7 cell line treated with 100nM E2 for 45 minutes in GSE59530 study. Table S10. Default binding affinity matrix of 6 samples by the 63,612 sites that overlap in at least two of the samples using DiffBind in (GSE94023, GSE99626, GSE67295, & GSE115607) MCF7 cell line treated with 10nM E2 for 45 minutes. Table S11. Default binding affinity matrix of 6 samples by the 23,517 sites that overlap in at least two of the samples using DiffBind in (GSE23893, GSE54855, & GSE59530) MCF7 cell line treated with 100nM E2 for 45 minutes. Table S12. Meta-differentially bound sites (meta-DBSs) obtained from a meta-analysis on (GSE94023, GSE99626, GSE67295, & GSE115607) MCF7 cell line treated with 10nM E2 for 45 minutes. Table S13. Meta-differentially bound sites (meta-DBSs) obtained from a meta-analysis on (GSE23893, GSE54855, & GSE59530) MCF7 cell line treated with 100nM E2 for 45 minutes. Table S14. literature_ChIP-seq. Table S15. Enrichr. Table S16. ARCHS4—Coexpression. Table S17. ENCODE--ChIP-seq. Table S18. ReMap--ChIP-seq. Table S19. GTEx—Coexpression. Table S20. Integrated_topRank. Table S21. Integrated_meanRank. Table S22. Gene Ontology (GO) for 7,308 meta-DBSs related to 617 common genes among MCF7 & T47D cell lines using Cistrome-GO. Table S23. KEGG pathways analysis for 7,308 meta-DBSs related to 617 common genes among MCF7 & T47D cell lines using Cistrome-GO. Table S24. Differentially expressed genes (DEGs) identified from GRO-seq data in the MCF7 cell line treated with 100nM E2 for 40 minutes in the GSE27463 study.

Tables display peak location and statistical comparisons, annotation of peak location, and data on nearest gene. (XLSX)

The columns show the differential region found and its closest gene. The information about the Peak is respectively the ID used internally (Internal ID), location of the peak (Chromosome name, start and end coordinates), width of the peak extension, attributes calculated by DiffBind (Concentration, Ty and MTy samples Concentration, Fold, p.value, FDR). DiffBind conc column show the mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) and the mean concentration over the first (Ty) group and second (MTy) group. The Fold column shows the difference in mean concentrations between the two groups (Conc_Ty–Conc_MTy), with a positive value indicating increased binding affinity in the Ty group and a negative value indicating increased binding affinity in the MTy group. The final two columns give confidence measures for identifying these sites as differentially bound, with a raw p-value and a multiple testing corrected FDR in the final column. The information about the feature is its location (chrm, start, end, strand) in genome, disposal of the peak in relation of the feature, distance of peak from start of the feature, shortest distance of peak from feature, feature identification in TriTrypDB database and feature name. Each Excel sheet is concern to Narrow or Broad regions. (XLSX)

Differential binding results of ChIP-seq datasets. Results from the differential binding analyses of the CTCF ChIP-seq dataset using csaw, and of the H3K4me3 and H3K27ac datasets using DiffBind. Format: xls. File size: 20.5Â MB. (XLS 20040 kb)

Peakwise_5hmC_Human_Obese_vs_Lean_MSCs_MitoCarta2.0_DBA_hMeDIPseq.diffbind.p1f0.all.sigsites.biomart.NormCounts

Annotated consensus peaks obtained from Diffbind across biological replicates for all modifications in female fru P1 neurons. (XLSB)

Annotated consensus peaks obtained from Diffbind across biological replicates for all modifications in male fru P1 neurons. (XLSB)

Additional file 6. Differentially accessible regions (peaks) from the EdgeR analysis within the Diffbind R package, between BRSV challenged and control calves (P