1 / 6

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

adele
Download Presentation

Evaluation of whole-community genome DNA amplification methods with microarrays

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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.

More Related