Evaluation and optimisation of preparative semi‐automated electrophoresis systems for Illumina library preparation

@article{Quail2012EvaluationAO,
  title={Evaluation and optimisation of preparative semi‐automated electrophoresis systems for Illumina library preparation},
  author={Michael A. Quail and Yong Gu and Harold P Swerdlow and Matthew Mayho},
  journal={ELECTROPHORESIS},
  year={2012},
  volume={33}
}
Size selection can be a critical step in preparation of next‐generation sequencing libraries. Traditional methods employing gel electrophoresis lack reproducibility, are labour intensive, do not scale well and employ hazardous interchelating dyes. In a high‐throughput setting, solid‐phase reversible immobilisation beads are commonly used for size‐selection, but result in quite a broad fragment size range. We have evaluated and optimised the use of two semi‐automated preparative DNA… Expand
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References

SHOWING 1-10 OF 22 REFERENCES
Large Scale Library Generation for High Throughput Sequencing
TLDR
The method utilizes selective precipitation of certain sizes of DNA molecules on to paramagnetic beads for cleanup and selection after standard enzymatic reactions to generate libraries for de novo and re-sequencing on the Illumina HiSeq 2000 instrument. Expand
Increased Throughput by Parallelization of Library Preparation for Massive Sequencing
TLDR
An automated parallel library preparation protocol using generic carboxylic acid-coated superparamagnetic beads and polyethylene glycol precipitation as a reproducible and flexible method for DNA fragment length separation is demonstrated, which enables a considerable efficiency increase for small to midsize sequencing centers. Expand
Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing
TLDR
The overall performance of all three methods was equal with only minor differences, and enzymatic fragmentation showed highest consistency between three library preparations but performed slightly worse than sonication and nebulization with regard to insertions/deletions in the raw sequence reads. Expand
Scalable Transcriptome Preparation for Massive Parallel Sequencing
TLDR
A method for automated library preparation of RNA prior to massively parallel sequencing is presented and shows consistent gene expression profiles in terms of sensitivity and quantification of gene expression between the two library preparation methods. Expand
Optimal enzymes for amplifying sequencing libraries
TLDR
To reduce bias, many thermostable DNA polymerases and alternate reaction conditions for amplification of adapter-ligated fragments for Illumina sequencing are investigated and a comparison to be relevant to other applications that involve simultaneous amplification of complex fragment mixtures. Expand
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes
TLDR
An amplification-free method of library preparation is presented, in which the cluster amplification step, rather than the PCR, enriches for fully ligated template strands, reducing the incidence of duplicate sequences, improving read mapping and single nucleotide polymorphism calling and aiding de novo assembly. Expand
Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries.
TLDR
For amplification of ancient DNA, it is found that some commonly used polymerases strongly bias against amplification of endogenous DNA in favor of GC-rich microbial contamination, in this case reducing the fraction of endogenous sequences to almost half. Expand
A large genome center's improvements to the Illumina sequencing system
TLDR
A set of improvements are described to the standard Illumina protocols to make the library preparation more reliable in a high-throughput environment, to reduce bias, tighten insert size distribution and reliably obtain high yields of data. Expand
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
TLDR
An improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate and identifies PCR during library preparation as a principal source of bias and optimized the conditions. Expand
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
TLDR
An automated, highly scalable method for carrying out the Solution Hybrid Selection capture approach that provides a dramatic increase in scale and throughput of sequence-ready libraries produced is presented. Expand
...
1
2
3
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