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

This dataset comprises single-cell RNA-sequencing data of two orthotopically xenografted desmoplastic small round cell tumor (DSRCT) cell lines (JN-DSRCT-1 and SK-DSRCT2) after posttranscriptional knockdown of EWSR1::WT1 fusion oncogene. Overall design: 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 in the peritoneum of 10–12 weeks old NOD/scid/gamma (NSG) mice. Seven-weeks after injection, mice were randomized in two groups and they were treated with either 2 mg/ml doxycycline (DOX) dissolved in drinking water containing 5% sucrose to induce an in vivo knockdown of WT1 (DOX (+)), or 5% sucrose (control, DOX (-)) for 96h. At the experimental endpoint mice were sacrificed by cervical dislocation.