Quantitative assessment of transcriptomic differences between ASPcKO and ASPcKOP7cKO flow cytometry-sorted murine FN-RMSs by RNA sequencing

We report the transcriptomic differences between ASPcKO and ASPcKOP7cKO flow cytometry-sorted FN-RMSs by RNA sequencing. The goal of this study is to determine what role Pax7 loss has on Pten-deficient, Hedgehog-activated murine FN-RMS tumors. These results provide implications for the transcriptomic program driven by Pax7 in dictating FN-RMS tumor fate. Overall design: Two different tumor models are described here - both driven by a constitutive, activated Smoothened allele (SmoM2) under the control of aP2-Cre. In one model, there is only the addition of Pten floxed alleles whereas in the other model there is Pten and Pax7 floxed alleles. A tdTomato allele is also bred into these mice to indelibly mark cells that have expressed aP2-Cre, For the experiment, four tumors from both tumor genotypes (ASPcKO and ASPcKOP7cKO) (8 total tumors) were flow cytometry-sorted and collected based on tdTomato+/PECAM1-APC-(negative) sorting to remove any endothelial cell contamination. These sorted tumor cells were then prepped for low input RNA sequencing.