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Nat Commun. 2017 Jul 24;8(1):105. doi: 10.1038/s41467-017-00136-z.

PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.

Bush EC1,2, Ray F1, Alvarez MJ1,3, Realubit R1,2, Li H1,2, Karan C1,2, Califano A4,5,6,7, Sims PA8,9,10.

Author information

1
Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA.
2
Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY, 10032, USA.
3
DarwinHealth Inc., New York, NY, 10032, USA.
4
Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA. andrea.califano@columbia.edu.
5
Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY, 10032, USA. andrea.califano@columbia.edu.
6
Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA. andrea.califano@columbia.edu.
7
Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA. andrea.califano@columbia.edu.
8
Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA. pas2182@cumc.columbia.edu.
9
Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY, 10032, USA. pas2182@cumc.columbia.edu.
10
Department of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, NY, 10032, USA. pas2182@cumc.columbia.edu.

Abstract

Pharmacological and functional genomic screens play an essential role in the discovery and characterization of therapeutic targets and associated pharmacological inhibitors. Although these screens affect thousands of gene products, the typical readout is based on low complexity rather than genome-wide assays. To address this limitation, we introduce pooled library amplification for transcriptome expression (PLATE-Seq), a low-cost, genome-wide mRNA profiling methodology specifically designed to complement high-throughput screening assays. Introduction of sample-specific barcodes during reverse transcription supports pooled library construction and low-depth sequencing that is 10- to 20-fold less expensive than conventional RNA-Seq. The use of network-based algorithms to infer protein activity from PLATE-Seq data results in comparable reproducibility to 30 M read sequencing. Indeed, PLATE-Seq reproducibility compares favorably to other large-scale perturbational profiling studies such as the connectivity map and library of integrated network-based cellular signatures.Despite the importance of pharmacological and functional genomic screens the readouts are of low complexity. Here the authors introduce PLATE-Seq, a low-cost genome-wide mRNA profiling method to complement high-throughput screening.

PMID:
28740083
PMCID:
PMC5524642
DOI:
10.1038/s41467-017-00136-z
[Indexed for MEDLINE]
Free PMC Article

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