Low-volume sequencing libraries from single cells
Echo Liquid Handlers miniaturize library preparation for whole genome and transcriptome analysis of genetic material from single cells. With precise, accurate, and non-contact transfer, Echo systems can reduce multiple displacement amplification (MDA) and RNA-Seq reactions by 75% or more. Libraries for next-generation sequencing (NGS) of RNA or DNA can be reduced to 10 µL or less.
Single-Cell Genomics is essential for the understanding of genetic and epigenetic variations that occur throughout the life of an organism. For example, cancer research programs are relying on single-cell genomics to overcome the challenges with data derived from heterogeneous tumor samples by studying individual cell types within a population and rare cell events.
Amplification of DNA from a single cell is inherently susceptible to contamination. Exogenous DNA from tips or nozzles used during the transfer of samples or reagents into a PCR reaction cannot be resolved with UV-irradiation steps. The Echo Liquid Handler's non-contact acoustic transfer completely avoids contact with any DNA to drastically lower contamination risk. Furthermore, the precision and accuracy of transfer at low nanoliter volumes, also reduce ongoing reagent costs.
By combining the Echo Liquid Handler's low-volume acoustic transfer capability with library preparation kits for RNA or DNA sequencing, researchers can drastically increase the number of libraries generated per kit. By cutting transfer volumes by 75% or more and pooling libraries for sequencing without iterative dilutions, Echo systems can miniaturize and improve the quality of libraries prepared from single cells.
by Amyris, Inc.
Elaine B. Shapland, Victor Holmes, Christopher D. Reeves, Elena Sorokin, Maxime Durot*, Darren Platt, Christopher Allen, Jed Dean, Zach Serber, Jack Newman, and Sunil Chandran
Amyris Inc., *TOTAL New Energies USA, Inc.
ABSTRACT: In recent years, next-generation sequencing (NGS) technology has greatly reduced the cost of sequencing whole genomes, whereas the cost of sequence verification of plasmids via Sanger sequencing has remained high. Consequently, industrialscale strain engineers either limit the number of designs or take short cuts in quality control. Here, we show that over 4000 plasmids can be completely sequenced in one Illumina MiSeq run for less than $3 each (15× coverage), which is a 20-fold reduction over using Sanger sequencing (2× coverage). We reduced the volume of the Nextera tagmentation reaction by 100-fold and developed an automated workflow to prepare thousands of samples for sequencing. We also developed software to track the samples and associated sequence data and to rapidly identify correctly assembled constructs having the fewest defects. As DNA synthesis and assembly become a centralized commodity, this NGS quality control (QC) process will be essential to groups operating high-throughput pipelines for DNA construction.