Additional file 5: Table S5. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

Comparison between our T-47D DNase-seq data and analogous data from ENCODE. DNase-seq peaks from promoter regions in BMP4-treated and vehicle-treated T-47D cells were compared to DNase-seq data of T-47D promoters from ENCODE (ENCSR000ELT replicates 1 and 2; ENCSR000EQB replicates 1 and 2). The table shows the percentage of shared peaks between pairs of samples. A high percentage of the peaks identified in our data are also present in ENCODE samples (cells B6-E7). (XLSX 8 kb

Additional file 3: Table S2. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

Differentially expressed genes after BMP4 treatment in T-47D cell line. Ensembl IDs, read counts, fold changes and Log2 ratios are shown. The genes are arranged in order from the largest to smallest Log2 ratio, first upregulated genes and then downregulated genes. (XLSX 34 kb

Additional file 2: Table S1. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

Differentially expressed genes after BMP4 treatment in MDA-MB-231 cell line. Ensembl IDs, read counts, fold changes and Log2 ratios are shown. The genes are arranged in order from the largest to smallest Log2 ratio, first upregulated genes and then downregulated genes. (XLSX 20 kb

Additional file 4: Table S3. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

Survival analysis of DEGs in MDA-MB-231. Table S4. Survival analysis of DEGs in T-47D. Each differentially expressed protein - coding gene was tested for possible association with the survival of breast cancer patients based on the gene expression data obtained from The Cancer Genome Atlas (TCGA). Blue background indicates DEGs shared by both cell lines. Benjamini-Hochberg corrected P-values are shown. No diff. = no association with survival. Not available = not found in TCGA data. (XLSX 16 kb

Additional file 9: Table S8. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

Primers used for DNase-seq. Table S9. Primer sequences for qRT-PCR based expression analyses of BMP4 target genes and transcription factors. (DOCX 19 kb

Additional file 8: Figure S3. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

Transcription factor validation. The chosen TFs were silenced and then treated with BMP4 before measuring target gene expression using qRT-PCR. The transcription factor and cell line in question is stated at the beginning of each page. DLL, which is downregulated in T-47D upon BMP4 treatment, is circled with red. (PDF 256 kb

Additional file 1: Figure S1. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

Relationship between chromatin status of TSS and gene expression. The boxplots illustrate the distribution of DNase-seq read coverage at TSS for protein-coding genes at five different levels of gene expression, which were determined by division of expressions into quintiles. Panel A shows the results obtained from untreated MDA-MB-231 cells and panel B the corresponding results for untreated T-47D cells. Panels C and D illustrate the difference between non-expressed and differentially expressed (protein - coding) genes in terms of the chromatin status at TSS in vehicle-treated samples of MDA-MB-231 and T-47D cells, respectively. In both cell lines, chromatin is clearly open at the TSS of differentially expressed genes before the stimulation with BMP4. (PDF 2463 kb