Preparation of Modified Combinatorial DNA Libraries via Emulsion PCR with Subsequent Strand Separation

2018 ◽  
Vol 52 (6) ◽  
pp. 854-864 ◽  
Author(s):  
S. A. Lapa ◽  
K. S. Romashova ◽  
M. A. Spitsyn ◽  
V. E. Shershov ◽  
V. E. Kuznetsova ◽  
...  
2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Eveline Farias-Hesson ◽  
Jonathan Erikson ◽  
Alexander Atkins ◽  
Peidong Shen ◽  
Ronald W. Davis ◽  
...  

Next-generation sequencing platforms are powerful technologies, providing gigabases of genetic information in a single run. An important prerequisite for high-throughput DNA sequencing is the development of robust and cost-effective preprocessing protocols for DNA sample library construction. Here we report the development of a semi-automated sample preparation protocol to produce adaptor-ligated fragment libraries. Using a liquid-handling robot in conjunction with Carboxy Terminated Magnetic Beads, we labeled each library sample using a unique 6 bp DNA barcode, which allowed multiplex sample processing and sequencing of 32 libraries in a single run using Applied Biosystems' SOLiD sequencer. We applied our semi-automated pipeline to targeted medical resequencing of nuclear candidate genes in individuals affected by mitochondrial disorders. This novel method is capable of preparing as much as 32 DNA libraries in 2.01 days (8-hour workday) for emulsion PCR/high throughput DNA sequencing, increasing sample preparation production by 8-fold.


PLoS ONE ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. e24910 ◽  
Author(s):  
Keke Shao ◽  
Weifeng Ding ◽  
Feng Wang ◽  
Haiquan Li ◽  
Da Ma ◽  
...  

2020 ◽  
Vol 46 (2) ◽  
pp. 264-268
Author(s):  
V. E. Kuznetsova ◽  
V. E. Shershov ◽  
R. A. Miftahov ◽  
S. A. Lapa ◽  
A. S. Zasedatelev ◽  
...  

2020 ◽  
Vol 117 (44) ◽  
pp. 27300-27306 ◽  
Author(s):  
Stanislav S. Terekhov ◽  
Igor E. Eliseev ◽  
Leyla A. Ovchinnikova ◽  
Marsel R. Kabilov ◽  
Andrey D. Prjibelski ◽  
...  

Conventional “bulk” PCR often yields inefficient and nonuniform amplification of complex templates in DNA libraries, introducing unwanted biases. Amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.


1998 ◽  
Vol 55 (6) ◽  
pp. 785
Author(s):  
Benjamin Joseph ◽  
Henry Furneaux

1986 ◽  
Vol 12 (3) ◽  
pp. 289-295 ◽  
Author(s):  
Bruno Baron ◽  
Philippe Métézeau ◽  
Didier Hatat ◽  
Christa Roberts ◽  
Michel E. Goldberg ◽  
...  

2004 ◽  
Vol 78 (5) ◽  
pp. 2502-2509 ◽  
Author(s):  
Linda Scobie ◽  
Samantha Taylor ◽  
James C. Wood ◽  
Kristen M. Suling ◽  
Gary Quinn ◽  
...  

ABSTRACT The potential transmission of porcine endogenous retroviruses (PERVs) has raised concern in the development of porcine xenotransplantation products. Our previous studies have resulted in the identification of animals within a research herd of inbred miniature swine that lack the capacity to transmit PERV to human cells in vitro. In contrast, other animals were capable of PERV transmission. The PERVs that were transmitted to human cells are recombinants between PERV-A and PERV-C in the post-VRA region of the envelope (B. A. Oldmixon, J. C. Wood, T. A. Ericsson, C. A. Wilson, M. E. White-Scharf, G. Andersson, J. L. Greenstein, H. J. Schuurman, and C. Patience, J. Virol. 76:3045-3048, 2002); these viruses we term PERV-A/C. This observation prompted us to determine whether these human-tropic replication-competent (HTRC) PERV-A/C recombinants were present in the genomic DNA of these miniature swine. Genomic DNA libraries were generated from one miniature swine that transmitted HTRC PERV as well as from one miniature swine that did not transmit HTRC PERV. HTRC PERV-A/C proviruses were not identified in the germ line DNAs of these pigs by using genomic mapping. Similarly, although PERV-A loci were identified in both libraries that possessed long env open reading frames, the Env proteins encoded by these loci were nonfunctional according to pseudotype assays. In the absence of a germ line source for HTRC PERV, further studies are warranted to assess the mechanisms by which HTRC PERV can be generated. Once identified, it may prove possible to generate animals with further reduced potential to produce HTRC PERV.


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