Dataset Information

Protein extraction in recalcitrant plant species

ABSTRACT: A possible approach for gel-based proteomic studies in recalcitrant woody plants, using phenol as the most suitable protein extraction method when working with tissues with high interfering compounds

INSTRUMENT(S): 4700 Proteomics Analyzer

ORGANISM(S): Pinus Pinaster (maritime Pine) Quercus Suber (cork Oak) Pisolithus Tinctorius Marx 270 Vitis Vinifera (grape)

SUBMITTER: Andreia Figueiredo

PROVIDER: PXD000224 | Pride | 2013-07-09

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 51

Publications

A possible approach for gel-based proteomic studies in recalcitrant woody plants.

Sebastiana Mónica M Figueiredo Andreia A Monteiro Filipa F Martins Joana J Franco Catarina C Coelho Ana Varela AV Vaz Fátima F Simões Tânia T Penque Deborah D Pais Maria Salomé MS Ferreira Sílvia S

SpringerPlus 20130508 1

Woody plants are particularly difficult to investigate due to high phenolic, resin, and tannin contents and laborious sample preparation. In particular, protein isolation from woody plants for two-dimensional gel electrophoresis (2-DE) is challenging as secondary metabolites negatively interfere with protein extraction and separation. In this study, three protein extraction protocols, using TCA, phenol and ethanol as precipitation or extraction agents, were tested in order to select the more eff ...[more]

PMID: 23724367

Similar Datasets

Project description:BackgroundThe 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.ResultsSILEX 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.ConclusionsA 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.

			Action	DRS
	F061144.dat	Other
	F061146.dat	Other
	F061147.dat	Other
	F061150.dat	Other
	F061151.dat	Other