scholarly journals High-Throughput DNA Extraction Method Suitable for PCR

BioTechniques ◽  
2003 ◽  
Vol 34 (4) ◽  
pp. 820-826 ◽  
Author(s):  
Zhanguo Xin ◽  
Jeff P. Velten ◽  
Melvin J. Oliver ◽  
John J. Burke
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
Dna Extraction Method

scholarly journals A new, harmless, high-throughput endosperm-based DNA extraction method for wheat

2019 ◽  
Vol 49 (9) ◽  
Author(s):  
Zhihui Ma ◽  
Yuquan Wang ◽  
Wenhui Wei ◽  
Zhengang Ru
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
Seedling Emergence ◽  
Control Group ◽  
Suitable Alternative ◽  
Dna Extraction Method ◽  
High Throughput Method ◽  
Young Leaves ◽  
Non Destructive

ABSTRACT: In this study, a non-destructive, high-throughput, endosperm-based DNA extraction method was developed. To verify the non-destructive nature of this method, a germination test was performed on 288 seeds after sampling their endosperm, which gave a seedling emergence rate that was higher (97.6%) than that of the control group (92%). To confirm the feasibility of the new method, DNA was extracted from plants of a BC1F2 population by two different methods, namely, from endosperm using our rapid, high-throughput method (ER-DNA) and from young leaves emerging from the same sampled seed using the CTAB method (LC-DNA). The ER-DNA was undetectable by agarose gel electrophoresis, but was found to be an adequate replacement for LC-DNA for the amplification and detection of simple sequence repeats (SSRs). Further analysis revealed that ER-DNA was generally suitable for the generation of specific 500-750-bp fragments, but not for the amplification of 1,000-2,000-bp fragments. Our rapid, high-throughput method therefore has no deleterious effects on wheat seeds and yields DNA for SSR genotyping that is a suitable alternative to traditionally obtained DNA.

scholarly journals SILEX: A fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

2020 ◽  
Author(s):  
santiago vilanova ◽  
David Alonso ◽  
Pietro Gramazio ◽  
Mariola Plazas ◽  
Edgar Garcia Fortea ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Next Generation Sequencing ◽  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
High Quality ◽  
Extraction Protocol ◽  
Dna Extraction Method ◽  
Sequencing Platforms ◽  
Generation Sequencing

Abstract Background The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. Results SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted from Solanum elaeagnifolium using this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. Conclusions A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.

scholarly journals A high throughput DNA extraction method from chemotypically heterogeneous plant species

2013 ◽  
Author(s):  
Parthadeb Ghosh ◽  
Parthadeb Ghosh ◽  
Sanjib Kumar Chattopadhyay ◽  
Sinchan Adhikari ◽  
Soumen Saha ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Plant Species ◽  
High Throughput ◽  
Extraction Method ◽  
Dna Extraction Method

scholarly journals Cost-Effective and Scalable DNA Extraction Method from Dried Blood Spots

2013 ◽  
Vol 59 (7) ◽  
pp. 1045-1051 ◽  
Author(s):  
Carlos A Saavedra-Matiz ◽  
Jason T Isabelle ◽  
Chad K Biski ◽  
Salvatore J Duva ◽  
Melissa L Sweeney ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Method ◽  
Low Cost ◽  
Melting Curve Analysis ◽  
Molecular Testing ◽  
High Quality ◽  
Congenital Diseases ◽  
Cell Counts ◽  
Dna Extraction Method

BACKGROUND Dried blood spot (DBS) samples have been widely used in newborn screening (NBS) for the early identification of disease to facilitate the presymptomatic treatment of congenital diseases in newborns. As molecular genetics knowledge and technology progresses, there is an increased demand on NBS programs for molecular testing and a need to establish reliable, low-cost methods to perform those analyses. Here we report a flexible, cost-efficient, high-throughput DNA extraction method from DBS adaptable to small- and large-scale screening settings. METHODS Genomic DNA (g.DNA) was extracted from single 3-mm diameter DBS by the sequential use of red cell lysis, detergent-alkaline, and acid-neutralizing buffers routinely used in whole blood and plant tissue DNA extractions. We performed PCR amplification of several genomic regions using standard PCR conditions and detection methods (agarose gel, melting-curve analysis, TaqMan-based assays). Amplicons were confirmed by BigDye® Terminator cycle sequencing and compared with reference sequences. RESULTS High-quality g.DNA was extracted from hundreds of DBS, as proven by mutation detection of several human genes on multiple platforms. Manual and automated extraction protocols were validated. Quantification of g.DNA by Oligreen® fluorescent nucleic acid stain demonstrated a normal population distribution closely corresponding with white blood cell counts detected in newborn populations. CONCLUSIONS High-quality, amplifiable g.DNA is extractable from DBSs. Our method is adaptable, reliable, and scalable to low- and high-throughput NBS at low cost ($0.10/sample). This method is routinely used for molecular testing in the New York State NBS program.

scholarly journals Protocol: a versatile, inexpensive, high-throughput plant genomic DNA extraction method suitable for genotyping-by-sequencing

Plant Methods ◽  
2018 ◽  
Vol 14 (1) ◽  
Author(s):  
Craig B. Anderson ◽  
Benjamin K. Franzmayr ◽  
Soon Won Hong ◽  
Anna C. Larking ◽  
Tracey C. van Stijn ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Genomic Dna ◽  
Extraction Method ◽  
Genotyping By Sequencing ◽  
Genomic Dna Extraction ◽  
Dna Extraction Method
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