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SEQUENCING

Low cost, highly efficient library preparation

HOME | APPLICATIONS | Sequencing

Low Cost, Highly Efficient Library Preparation

Echo Liquid Handlers enable library preparation in low microliter volumes for a range of sequencing methods including Sanger, 16S, and Next-Gen Sequencing (NGS) – to dramatically reduce reagent costs, save samples, and eliminate steps — all while improving library quality and throughput.


With Sanger sequencing, BigDye reagent costs can be a limiting factor. Sequencing volumes can be reduced from 10 µL to 2.5 µL with the use of the Echo Liquid Handler for over a 4-fold reduction in cost per reaction.


16S sequencing has long been the method of choice for microbiome researchers. The use of the Echo Liquid Handler allows for miniaturized 16S sequencing, and the reagent cost reduction is also enabling researchers to shift to miniaturized shotgun sequencing.

Reduce Library Prep Costs 100-Fold

Use of the Echo Liquid Handler for NGS library preparation versus conventional liquid handlers allows for up to a 100-fold reduction in reaction volumes, dramatically reducing study reagent costs.



Comparison of Liquid Handling Methods

  Manual Pipetting Echo® Liquid Handler
Amount of DNA 50 ng 0.06 – 2.0 ng
DNA volume (Rxn) 25 µL 200 nL
Library prep volume (Rxn) 25 µL 300 nL
Total volume 50 µL 0.5 µL
Reactions per kit 96 9600
Cost per reaction $72.91 $0.73
Echo 525 Liquid Handler
Echo® 525 LIQUID HANDLER

Reduce Transfer Volumes by 75% or More

When NGS sequencing programs scale, the cost of sample preparation is a limiting factor. The Echo Liquid Handlers offer an opportunity to scale with confidence. By combining the Echo Liquid Handler's low-volume acoustic transfer capability with Illumina's Nextera XT library preparation kit, researchers can drastically increase the number of libraries generated. Whether using the Nextera XT kit for amplicon, plasmid, or small genome sequencing, the Echo system can reduce transfer volumes by 75% or more. The same benefits can be realized with sample preparation kits from Kapa, NEB, NuGEN, and others.

USER TESTIMONIAL

“By using the Echo 525, a scale-down by 50 – 100x can be achieved with minor modifications of the protocol, leading to significant cost reduction without sacrificing data quality. Furthermore, we demonstrate the superiority of contact-free liquid transfers in molecular biology applications with regard to reproducibility and contamination prevention.”

Stephan Lorenz  |  Wellcome Trust Sanger Institute, UK


Pool Libraries for Sequencing with Greater Accuracy in Less Time

Echo Liquid Handlers can rapidly pool and normalize oligos or DNA libraries from any well of a microplate. With average transfer times of no more than a few seconds per well. Echo Liquid Handlers can reduce pooling times by more than 80% compared to traditional liquid handlers. Since Echo systems can transfer volumes as little as 2.5 nanoliters, high concentration libraries do not have to be diluted prior to transfer. This capability results in simultaneous normalization while pooling. Furthermore, by avoiding tip-based sample dilution, the propagation of errors from sample retention by tips is eliminated. This drastically improves the concentration accuracy of all libraries pooled.



FEATURED PUBLICATION

Low-cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process

Low-cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process

by Amyris, Inc.
December 2014

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.

VIEW / DOWNLOAD PDF





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.



Key Benefits

  • Reduced operating costs through efficient assay miniaturization
  • Improved data quality with assay volumes as low as 250 nL
  • Elimination of cross contamination
  • Integrated systems and software tailored for genomic assays



Featured App Note
FEATURED VIDEOS
DOWNLOAD BROCHURES
  • Echo Liquid Handler
    Echo®
    Liquid Handlers
    Acoustic liquid transfer technology
    DOWNLOAD
  • Access Laboratory Workstation
    Access™
    Laboratory Workstation
    Walk-up automation for Echo Liquid Handlers
    DOWNLOAD
  • Labcyte Consumables
    Labcyte®
    Consumables
    Precision manufacturing, exceptional performance
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ACCESS CONFIGURATIONS
  • Access Workstation for Genomics
    Access™
    Workstation for Genomics
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APPLICATION NOTES
FEATURED POSTERS
For Research Use Only Not for use in Diagnostics