Author:
Li Jingyao,Ho Daniel J.,Henault Martin,Yang Chian,Neri Marilisa,Ge Robin,Renner Steffen,Mansur Leandra,Lindeman Alicia,Tumkaya Tayfun,Russ Carsten,Hild Marc,Keller Caroline Gubser,Jenkins Jeremy L.,Worringer Kathleen A.,Sigoillot Frederic D.,Ihry Robert J.
Abstract
AbstractUnbiased transcriptomic RNA-seq data has provided deep insights about biological processes. However, its impact in drug discovery has been narrow given high costs and low throughput. Proof-of-concept studies with Digital RNA with pertUrbation of Genes (DRUG)-seq demonstrated the potential to address this gap. We extended the DRUG-seq platform by subjecting it to rigorous testing and by adding an open-source analysis pipeline. The results demonstrate high reproducibility and ability to resolve the mechanism(s) of action for a diverse set of compounds. Overall, the protocol and open-source analysis pipeline are a step towards industrializing RNA-seq for high complexity transcriptomics studies performed at a saturating scale.
Publisher
Cold Spring Harbor Laboratory
Reference27 articles.
1. Becht, E. , Mcinnes, L. , Healy, J. , Dutertre, C. , Kwok, I.W.H. , Ng, L.G. , Ginhoux, F. , and Newell, E.W. (2019). Dimensionality reduction for visualizing single-cell data using UMAP. Nat. Biotechnol. 37.
2. Fast unfolding of communities in large networks
3. Bush, E.C. , Ray, F. , Alvarez, M.J. , Realubit, R. , Li, H. , Karan, C. , Califano, A. , and Sims, P.A. (2017). PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens. Nat. Commun. 8.
4. Efficient Generation of Transcriptomic Profiles by Random Composite Measurements
5. Consortium, S.W.G. of the P.G. , Ripke, S. , Walters, J.T. , and O’Donovan, M.C. (2020). Mapping genomic loci prioritises genes and implicates synaptic biology in schizophrenia. MedRxiv 2020.09.12.20192922.
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
1. Gene Signature-Based Drug Repositioning;Drug Repurposing - Molecular Aspects and Therapeutic Applications [Working Title];2021-12-02