Additional file 1: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

Full information regarding the mRNA microarray gene expression datasets used in this study. The dataset title is used in the text as a dataset identifier. (PDF 171 kb

Additional file 6: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

Description of gene clusters identified by the time clusterization analysis. (XLSX 415 kb

Additional file 5: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

Results of the enrichment analysis of genes that were differentially expressed in response to different stress factors. (XLSX 171 kb

Additional file 2: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

Supplementary materials and methods. (PDF 151 kb

Additional file 4: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

Figure S1. PCA clustering of splicing inclusion level differences between treated and untreated PDX tumors. Figure S2: Graph representing the common transcription factors GFI1B (A) and TARDBP (B) that may induce concerted changes in the expression of pairs of splicing- and mitotic-related genes after a course of chemotherapy. Solid black lines connect a pair of co-expressed genes and red lines connect transcription factors with their target genes. Figure S3: Western blotting analysis of U87MG cells and their concentrated secretomes before and after treatment with 30 μM Cisplatin (CP). Figure S4: Pladienolide B increases the sensitivity of cancer cells to Cisplatin. (A) Viability assay of U87MG, Hela and MCF-7 cells that were pretreated with 2 nM Pladienolide B (2 days) following treatment with different concentrations of Cisplatin (4 days). (B) FACS analysis of caspase 3/7 and SYTOX staining of SKOV3 cells treated with 0.5 nM Pladienolide B, 10 μM Cisplatin or both drugs together. (C) Cell cycle analysis of SKOV3 and HT29 cells treated for 3 days with 0.5 nM and 1 nM Pladienolide B, respectively. (D) FACS analysis of phospho ATM staining in Hela, A549 and HT29 cells that were cultivated with 1 nM Pladienolide B (2 days) and subsequently treated with the indicated concentrations of Cisplatin (1 day). (PDF 855 kb

Additional file 3: of Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

(A) Description of all alternative splicing events in cancer cell lines after therapy. (B) Identification of stop codons in transcripts with retained introns, which were detected in at least half of cancer cell lines before and after chemotherapy. (C) Description of all alternative splicing events in PDX tumors after different types of therapy. (D) Identification of stop codons in transcripts with retained introns, which were detected in PDX tumors before and after chemotherapy. (E) Description of alternative splicing events in spliceosomal genes in PDX tumors after different types of therapy. (F) Description of insertions which were detected in 7 cell lines (A375, A549, H3122, N87, PC9, RT112, H358) used in our analysis of alternative splicing changes. (XLSX 716 kb