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A tunable filter for high molecular weight DNA selection and linked-read sequencing
- Source :
- Lab on a Chip, Lab on a Chip, Royal Society of Chemistry, 2020, 20 (1), pp.175-184. ⟨10.1039/C9LC00965E⟩, Lab on a Chip, Royal Society of Chemistry, 2020, ⟨10.1039/C9LC00965E⟩, Lab on a Chip, 2020, 20 (1), pp.175-184. ⟨10.1039/C9LC00965E⟩
- Publication Year :
- 2020
- Publisher :
- Royal Society of Chemistry (RSC), 2020.
-
Abstract
- International audience; In third generation sequencing, the production of quality data requires the selection of molecules longer than ∼20 kbp, but the size selection threshold of most purification technologies is smaller than this target. Here, we describe a technology operated in a capillary with a tunable selection threshold in the range of 3 to 40 kbp controlled by an electric field. We demonstrate that the selection cut-off is sharp, the purification yield is high, and the purification throughput is scalable. We also provide an analytical model that the actuation settings of the filter. The selection of high molecular weight genomic DNA from the melon Cucumis melo L., a diploid organism of ∼0.45 Gbp, is then reported. Linked-read sequencing data show that the N50 phase block size, which scores the correct representation of two chromosomes, is enhanced by a factor of 2 after size selection, establishing the relevance and versatility of our technology.
- Subjects :
- Computer science
Sequencing data
Biomedical Engineering
Bioengineering
02 engineering and technology
Third generation sequencing
Computational biology
Biochemistry
[SPI.MAT]Engineering Sciences [physics]/Materials
03 medical and health sciences
Cucumis melo
Particle Size
[PHYS.COND]Physics [physics]/Condensed Matter [cond-mat]
Throughput (business)
ComputingMilieux_MISCELLANEOUS
Selection (genetic algorithm)
030304 developmental biology
0303 health sciences
DNA
Sequence Analysis, DNA
General Chemistry
021001 nanoscience & nanotechnology
Molecular Weight
genomic DNA
Filter (video)
[SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic
0210 nano-technology
Block size
High molecular weight dna
Subjects
Details
- ISSN :
- 14730189 and 14730197
- Volume :
- 20
- Database :
- OpenAIRE
- Journal :
- Lab on a Chip
- Accession number :
- edsair.doi.dedup.....2ffc272736ebef73ca83c6e29fbca888