Super-enhancer-driven CACNA2D2 is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT) [Affymetrix]

This dataset comprises transcriptome data of two subcutaneously xenografted desmoplastic small round cell tumor (DSRCT) cell lines (JN-DSRCT-1 and SK-DSRCT2) after posttranscriptional knockdown of EWSR1::WT1 fusion oncogene for 96h. Two desmoplastic small round cell tumor (DSRCT) cell lines were stably transduced with inducible shRNA expressing casettes targeting either the CDS (shWT1-CDS) or 3'-UTR (shWT1-UTR) of the EWSR1::WT1 fusion transcript. One million DSRCT cells harboring either shRNA against WT1-CDS or WT1-UTR were resuspended in PBS and mixed with Geltrex™ LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix in 1:1 proportion, and slowly injected subcutaneously in the right flank of 10–12 weeks old NOD/scid/gamma (NSG) mice. When the tumors reached an average volume of 80 mm3, mice were randomized into two groups. 96h prior to the pre-determined end of the experiment, mice were treated with either 2 mg/ml doxycycline (DOX) dissolved in drinking water containing 5% sucrose to induce an in vivo knockdown of EWSR1::WT1 (DOX (+)), or 5% sucrose (control, DOX (−)). At the experimental endpoint the mice were sacrificed by cervical dislocation. Then, subcutaneous xenografted tumors were extracted and used for total RNA extraction. RNA was isolated from 16 xenografts, two xenografts per shRNA and per cell line from mice treated with DOX and from control mice. The transcriptome was profiled on GeneChip™ Human Genome U133 Plus 2.0 Array. Raw data were processed applying the Robust Multi-chip Average (RMA) algorithm, including background adjustment, quantile normalization and summarization. For RMA normalization custom brainarray Chip Description Files (CDF; ENTREZG, v25) were used, yielding one optimized probe set per gene.