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Transcript
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: [email protected] S1 A Ratio of signal intensity of amplified to unamplified DNA Unamplified Bst Genes Genes B Unamplified Genes Desulfovibrio vulgaris Hildenborough REPLI-g Genes Templiphi Genes Rhodopseudomonas palustris CGA009 Bst Genes REPLI-g Genes Templiphi Genes S2 C Ratio of signal intensity of amplified to unamplified DNA Unamplified Bst Genes Genes D Unamplified Genes Shenwanella oneidensis MR-1 REPLI-g Genes Templiphi Genes Thermoanaerobacter ethanolicus X514 Bst Genes REPLI-g Genes Templiphi 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. S3 Ratio of signal intensity of amplified to unamplified DNA 10 Bst REPLI-g Templiphi 1 0.1 Bst_S Genes REPLI-g_S Genes Templiphi_S 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-g and sonicated before labeling, Templiphi: amplified with Templiphi, Templiphi_S. S4 4 Bst vs Templiphi Bst vs REPLI-g 1 0.125 4 4 REPLI-g vs Templiphi 1 1 8 0.125 1 1 8 0.125 1 8 R² = 0.1376 0.25 R² = 0.1742 0.25 R² = 0.1393 0.25 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. S5 Rep1 vsRep2 Rep2 vsRep3 4 1 1 0.25 4 1 4 0.25 1 4 R² = 0.965 R² = 0.9679 0.25 0.25 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. S6
