Evaluation of whole-community genome DNA amplification methods with microarrays

Jian Wang 1, 2, Joy D. Van Nostrand 2, 3, Liyou Wu 2, 3, Zhili He 2, 3, Guanghe Li 1 , and Jizhong Zhou 1, 2, 3, *

Supplemental materials

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1 School of Environment, Tsinghua University, Beijing, China2 Institute for Environmental Genomics, University of Oklahoma, Norman, OK3 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

*Corresponding author: Dr. Jizhong Zhou Institute for Environmental Genomics (IEG) Department of Botany and Microbiology University of Oklahoma Norman, OK 73019 Phone: 405-325-6073

Fax: 405-325-7552 E-mail: jzhou@ou.edu

Rhodopseudomonas palustris CGA009B

Unamplified Bst REPLI-g

Unamplified Bst REPLI-g

A Desulfovibrio vulgaris Hildenborough

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GenesGenes Genes

GenesGenes Genes

Templiphi

Genes

Templiphi

Genes

Thermoanaerobacter ethanolicus X514

C

D

Unamplified Bst REPLI-g

Unamplified Bst REPLI-g

Shenwanella oneidensis MR-1

FIG. S1. Ratio of signal intensity of Cy5 to Cy3 (unamplfied DNA, DNA amplified by Bst, REPLI-g and Templiphi to unamplified DNA) of individual gene for pure culture genome. (A) Desulfovibrio vulgaris Hildenborough, (B) Rhodopseudomonas palustris CGA009, (C) Shenwanella oneidensis MR-1 and (D) Thermoanaerobacter ethanolicus X514.

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GenesGenes Genes

GenesGenes Genes

Genes

Templiphi

Genes

Templiphi

FIG. S2. Ratio of signal intensity of amplified to unamplified DNA (DNA amplified by Bst, REPLI-g and Templiphi to unamplified DNA) of individual gene detected by GeoChip for the community sample. 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.

0.1

1

10Bst REPLI-g

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Bst_S REPLI-g_S

Genes Genes

Templiphi

Genes

Templiphi_S

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FIG. S3. Scatter plot of Cy5/Cy3 ratios of biased genes in aDNA amplified by the three MDA methods. DNA of Shenwanella oneidensis MR-1 was used as the template. The genes whose Cy5/Cy3 ratios in any aDNA showed >1 fold are defined as biased genes. The results suggested that the different MDA methods would produce different biased genes.

R² = 0.1376

0.25

1

4

0.125 1 8

Bst vs REPLI-g

R² = 0.17420.25

1

4

0.125 1 8

Bst vs Templiphi

R² = 0.13930.25

1

4

0.125 1 8

REPLI-g vs Templiphi

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FIG. S4. Scatter plot of Cy5/Cy3 ratio of biased genes in aDNA amplified by Bst in different technical replicates. DNA of Shenwanella oneidensis MR-1 was used as the template. The genes whose Cy5/Cy3 ratios in any replicates showed >1 fold are defined as biased genes. The results suggested that the bias produced by one MDA method would be reproducible.

R² = 0.965

0.25

1

4

0.25 1 4

Rep1 vsRep2

R² = 0.9679

0.25

1

4

0.25 1 4

Rep2 vsRep3