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Genome Biol. 2019 Aug 6;20(1):155. doi: 10.1186/s13059-019-1748-6.

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis.

Author information

1
Institute of Stem Cell Research, Helmholtz Center Munich, 85764, Neuherberg, Germany.
2
Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
3
Institute of Computational Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany.
4
Department of Mathematics, Technical University Munich, 85748, Garching, Germany.
5
Institute of Computational Biology, Helmholtz Center Munich, 85764, Neuherberg, Germany. nikola.mueller@helmholtz-muenchen.de.
6
Institute of Stem Cell Research, Helmholtz Center Munich, 85764, Neuherberg, Germany. micha.drukker@helmholtz-muenchen.de.

Abstract

We describe a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts or genomic regions from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, which are all pre-selected and optimized in silico. By applying the matrices in a novel workflow named Barcode Assembly foR Targeted Sequencing (BART-Seq), we analyze developmental states of thousands of single human pluripotent stem cells, either in different maintenance media or upon Wnt/β-catenin pathway activation, which identifies the mechanisms of differentiation induction. Moreover, we apply BART-Seq to the genetic screening of breast cancer patients and identify BRCA mutations with very high precision. The processing of thousands of samples and dynamic range measurements that outperform global transcriptomics techniques makes BART-Seq first targeted sequencing technique suitable for numerous research applications.

KEYWORDS:

Barcoding; High-throughput screening; Human pluripotent stem cells; Multiplex PCR; Single-cell RNA sequencing; Targeted transcriptomics

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