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 - PowerPoint PPT Presentation
6
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 S1 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
Transcript
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
S1
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
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
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
S4
Bst_S REPLI-g_S
Genes Genes
Templiphi
Genes
Templiphi_S
vicle
Reviewer1:The ratio of signal intensity of amplified to unamplified DNA for which “individual gene” is plotted here? A: The individual genes were the functional genes of the community sample dectecd by GeoChip, including genes related to C,N,P,S cycling, metal resistance and organic compounds degradation.
S5
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
S6
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.
