Transcriptomics following CRISPR KO of individual DUBs or inhibition of DUBs with small molecule inhibitors. Transcriptomics following CRISPR KO of individual DUBs or inhibition of DUBs with small molecule inhibitors

CRISPR KO RNA-seq data: To generate knockouts, we used a commercially available arrayed CRISPR-Cas9 library targeting 81 out of ~100 DUBs and 13 additional proteins in the ubiquitin-proteasome system, including ubiquitin-like proteins; the library was constructed with four, pooled, guides per target. mRNA profiling was performed 96 hours after guide RNA transfection using a high-throughput, low-cost RNA-sequencing method (3’ Digital Gene Expression or 3’DGE-seq) in the MDAMB231 breast cancer cell line. Inhibitor RNA-seq data: For the small molecule inhibitor signatures, MDAMB231 or MCF7 or MCF7 TP53 shRNA breast cancer cells were treated with a panel of DUB inhibitors for 24 hours, then 3'DGE-seq was used to perform the mRNA profiling. Overall design: mRNA profiles following DUB KO or DUB inhibition with small molecule inhibitors