DOI: 10.5061/dryad.cz8w9gjb4
title: Data from: Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform

description: The majority of cancer deaths are caused by solid tumors, where the four
 most prevalent cancers (breast, lung, colorectal and prostate) account for
 more than 60% of all cases (1). Tumor cell heterogeneity driven by
 variable cancer microenvironments, such as hypoxia, is a key determinant
 of therapeutic outcome. We developed a novel culture protocol, termed the
 Long-Term Hypoxia (LTHY) time course, to recapitulate the gradual
 development of severe hypoxia seen in vivo to mimic conditions observed in
 primary tumors. Cells subjected to LTHY underwent a non-canonical
 epithelial to mesenchymal transition (EMT) based on miRNA and mRNA
 signatures as well as displayed EMT-like morphological changes.
 Concomitant to this, we report production of a novel truncated isoform of
 WT1 transcription factor (tWt1), a non-canonical EMT driver, with
 expression driven by a yet undescribed intronic promoter through
 hypoxia-responsive elements (HREs). We further demonstrated that tWt1
 initiates translation from an intron-derived start codon, retains proper
 subcellular localization and DNA binding. A similar tWt1 is also expressed
 in LTHY-cultured human cancer cell lines as well as primary cancers and
 predicts long-term patient survival. Our study not only demonstrates the
 importance of culture conditions that better mimic those observed in
 primary cancers, especially with regards to hypoxia, but also identifies a
 novel isoform of WT1 which correlates with poor long-term survival in
 ovarian cancer.
description: # Data from: Long-term severe hypoxia adaptation induces non-canonical EMT
 and a novel Wilms Tumor 1 (WT1) isoform
 [https://doi.org/10.5061/dryad.cz8w9gjb4](https://doi.org/10.5061/dryad.cz8w9gjb4) Contains RNASeq, ChIPSeq, Mass Spectrometry, and gPCR datasets used for the publication: Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform. ## Description of the data and file structure Each file corresponds to a separate dataset.  RNASeq:     DEG_0.1vs5.complete.txt is the RNASeq file for long RNASeq analysis done during LTHY incubation (please refer to publication for methodology details). Sample names correspond to oxygen exposure levels. Table is DESeq2 processed output. Statistics were calculated comparing the beginning and the end of the experiment (5% oxygen vs 0.1% oxygen)     miRs_0.1vs5.complete.txt is the RNAseq file for the same experiment as the DEG file. Sample naming conversion and file generation was the same as the DEG file. Refer to publication for detailed methodology ChIPSeq:     tWT1-GFP_ChIPseq.csv is a tab separated file describing the ChIPSeq peaks found when expressing a truncated version of WT1 under hypoxia. This truncated WT1 isoform is reffered to in the table as "KTSminus". Negative control is a non-functional version of WT1 reffered to as tWT1.2 in the publication and as wt_wtout in the data table. Mass Spectrometry:     MS_data_table.xlsx contains peptide coverage for truncated WT1 protein expression. gPCR dataset:     zip file contains Sanger sequencing results regarding loci of interest around the WT1 gene in B16-HG cells. ## Code/Software Code used in the analysis of this dataset is available upon request