Datasets Used in Evaluation Of RNAi And CRISPR Technologies By Large Scale Gene Expression Profiling In The Connectivity Map

ABSTRACT: This GEO Series contains datasets used in the paper "Evaluation Of RNAi And CRISPR Technologies By Large Scale Gene Expression Profiling In The Connectivity Map". The application of RNA interference (RNAi) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes. Although RNAi has revolutionized loss of function genetic experiments, it has been difficult to systematically assess the prevalence and consequences of off-target effects. The Connectivity Map (CMAP) represents an unprecedented resource to study the gene expression consequences of expressing short hairpin RNAs (shRNAs). Analysis of signatures for over 13,000 shRNAs applied in 9 cell lines revealed that miRNA-like off-target effects of RNAi are far stronger and more pervasive than generally appreciated. We show that mitigating off-target effects is feasible in these datasets via computational methodologies to produce a Consensus Gene Signature (CGS). In addition, we compared RNAi technology to clustered regularly interspaced short palindromic repeat (CRISPR)-based knockout by analysis of 373 sgRNAs in 6 cells lines, and show that the on-target efficacies are comparable, but CRISPR technology is far less susceptible to systematic off-target effects. These results will help guide the proper use and analysis of loss-of-function reagents for the determination of gene function. Note: Related GEO projects include a large corpus of additional L1000 data, available at GSE92742. The Platform is GPL20573: Broad Institute Human L1000 epsilon https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573 For questions or assistance with this dataset, please email the CMap support team at: [e-mail]

ORGANISM(S): Homo sapiens

PROVIDER: GSE106127 | GEO | 2017/10/30

REPOSITORIES: GEO