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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE187008 | GEO | 2021/11/03

REPOSITORIES: GEO

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