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Evaluation of whole-community genome DNA amplification methods with microarrays

Supplemental materials. 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, *. 1 School of Environment, Tsinghua University, Beijing, China

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Evaluation of whole-community genome DNA amplification methods with microarrays

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  1. Supplemental materials 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, * 1 School of Environment, Tsinghua University, Beijing, China 2 Institute for Environmental Genomics, University of Oklahoma, Norman, OK 3 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

  2. A Desulfovibrio vulgaris Hildenborough Unamplified Templiphi Bst REPLI-g Ratio of signal intensity of amplified to unamplified DNA Genes Genes Genes Genes Genes Genes Genes B Rhodopseudomonas palustris CGA009 Templiphi Unamplified Bst REPLI-g Genes

  3. Shenwanella oneidensis MR-1 C Templiphi Unamplified Bst REPLI-g Ratio of signal intensity of amplified to unamplified DNA Genes D Thermoanaerobacter ethanolicus X514 Genes Genes Genes Genes Genes Genes Templiphi Unamplified Bst REPLI-g Genes 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.

  4. Templiphi Ratio of signal intensity of amplified to unamplified DNA Bst REPLI-g Templiphi_S Bst_S REPLI-g_S Genes Genes Genes 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-gand sonicated before labeling, Templiphi: amplified with Templiphi, Templiphi_S.

  5. FIG. S3. Scatterplot 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.

  6. FIG. S4. Scatterplot 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.

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