Microarray-based evaluation of whole-community genome DNA amplification methods - PubMed (original) (raw)

Microarray-based evaluation of whole-community genome DNA amplification methods

Jian Wang et al. Appl Environ Microbiol. 2011 Jun.

Abstract

Three whole-community genome amplification methods, Bst, REPLI-g, and Templiphi, were evaluated using a microarray-based approach. The amplification biases of all methods were <3-fold. For pure-culture DNA, REPLI-g and Templiphi showed less bias than Bst. For community DNA, REPLI-g showed the least bias and highest number of genes, while Bst had the highest success rate and was suitable for low-quality DNA.

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Figures

Fig. 1.

Fig. 1.

Outline of evaluation of three MDA methods using pure cultures (a) and a community sample (b). gDNA, unamplified genomic DNA; aDNA, amplified DNA.

Fig. 2.

Fig. 2.

Yields of the three amplification methods for pure culture and community DNA. Error bars represent the standard deviations of the results for 3 replicates.

Fig. 3.

Fig. 3.

Hierarchical cluster analysis of amplified and unamplified community DNA based on GeoChip results. gDNA, unamplified DNA; Bst, amplified with Bst; Bst_S, amplified with Bst and sonicated before labeling; REPLI-g, amplified with REPLI-g; REPLI-g_S, amplified with REPLI-g and sonicated before labeling; Templiphi, amplified with Templiphi; Templiphi_S, amplified with Templiphi and sonicated before labeling.

Fig. 4.

Fig. 4.

Relative abundance of all functional gene categories (a) and microbial classes (b) detected by GeoChip in gDNA and aDNA. Relative abundance was calculated based on the gene number. Bars: 1, gDNA; 2, aDNA amplified with Bst; 3, aDNA amplified with Bst and sonicated before labeling; 4, aDNA amplified with REPLI-g; 5, aDNA amplified with REPLI-g and sonicated before labeling; 6, aDNA amplified with Templiphi; 7, aDNA amplified with Templiphi and sonicated before labeling.

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