Transcript Bst polymerase for whole genome amplification

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