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

Autor: Can Sönmezer, Fabian J. Theis, Florian Opperer, Micha Drukker, Christian Krendl, Dmitry Shaposhnikov, Nikola S. Mueller, Steffen Sass, Fatma Uzbas, Philipp Angerer
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Pluripotent Stem Cells
lcsh:QH426-470
Targeted transcriptomics
Cost-Benefit Analysis
In silico
High-throughput screening
Method
Breast Neoplasms
Genomics
Computational biology
Biology
Barcode
Workflow
law.invention
Single-cell RNA sequencing
03 medical and health sciences
0302 clinical medicine
Single-cell analysis
law
Multiplex polymerase chain reaction
Humans
Human pluripotent stem cells
Induced pluripotent stem cell
Wnt Signaling Pathway
lcsh:QH301-705.5
Embryonic Stem Cells
030304 developmental biology
Barcoding
0303 health sciences
Single-cell Rna Sequencing
Targeted Transcriptomics
High-throughput Screening
Human Pluripotent Stem Cells
Multiplex Pcr
Sequence Analysis
RNA
Gene Expression Profiling
High-Throughput Nucleotide Sequencing
Multiplex PCR
Human genetics
ddc
lcsh:Genetics
lcsh:Biology (General)
Female
Single-Cell Analysis
030217 neurology & neurosurgery
Zdroj: Genome Biology, Vol 20, Iss 1, Pp 1-16 (2019)
Genome Biology
Genome Biol. 20:155 (2019)
DOI: 10.1186/s13059-019-1748-6
Popis: 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. Electronic supplementary material The online version of this article (10.1186/s13059-019-1748-6) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
Externí odkaz: