1. 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 S1S1 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. Rhodopseudomonas palustris CGA009B Unamplified BstREPLI-g Unamplified BstREPLI-g ADesulfovibrio vulgaris Hildenborough Ratio of signal intensity of amplified to unamplified DNA S2S2 Genes Templiphi Genes Templiphi Genes

3. Ratio of signal intensity of amplified to unamplified DNA Thermoanaerobacter ethanolicus X514 C D Unamplified BstREPLI-g Unamplified BstREPLI-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. S3S3 Genes Templiphi Genes Templiphi

4. 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. Ratio of signal intensity of amplified to unamplified DNA BstREPLI-g S4S4 Bst_SREPLI-g_S Genes Templiphi Genes Templiphi_S

5. S5S5 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.

6. S6S6 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.