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BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis.
- Source :
-
Genome biology [Genome Biol] 2019 Aug 06; Vol. 20 (1), pp. 155. Date of Electronic Publication: 2019 Aug 06. - Publication Year :
- 2019
-
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.
- Subjects :
- Breast Neoplasms genetics
Cost-Benefit Analysis
Embryonic Stem Cells metabolism
Female
Gene Expression Profiling economics
Genomics economics
High-Throughput Nucleotide Sequencing economics
Humans
Pluripotent Stem Cells metabolism
Sequence Analysis, RNA economics
Single-Cell Analysis economics
Single-Cell Analysis methods
Wnt Signaling Pathway
Workflow
Gene Expression Profiling methods
Genomics methods
High-Throughput Nucleotide Sequencing methods
Sequence Analysis, RNA methods
Subjects
Details
- Language :
- English
- ISSN :
- 1474-760X
- Volume :
- 20
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Genome biology
- Publication Type :
- Academic Journal
- Accession number :
- 31387612
- Full Text :
- https://doi.org/10.1186/s13059-019-1748-6