Open Access Highly Accessed Research article

Using pyrosequencing to shed light on deep mine microbial ecology

Robert A Edwards1234*, Beltran Rodriguez-Brito13, Linda Wegley1, Matthew Haynes1, Mya Breitbart1, Dean M Peterson5, Martin O Saar6, Scott Alexander6, E Calvin Alexander6 and Forest Rohwer12

Author Affiliations

1 Department of Biology, San Diego State University, San Diego, USA.

2 Center for Microbial Sciences, San Diego State University, San Diego, USA.

3 Computational Science Research Center, San Diego State University, San Diego, USA.

4 Fellowship for Interpretation of Genomes, Burr Ridge, USA.

5 Natural Resources Research Institute, Department of Geological Sciences, University of Minnesota, Duluth, USA.

6 Department of Geology and Geophysics, University of Minnesota, Minneapolis, USA.

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BMC Genomics 2006, 7:57  doi:10.1186/1471-2164-7-57

Published: 20 March 2006

Additional files

Additional File 6:

A gzip compressed archive of the fasta files (those ending .fa.gz) and quality scores (those ending .qual.gz) of sequences from the Red samples as supplied by 454, Inc.

Format: ZIP Size: 33.9MB Download file

Open Data

Additional File 7:

A gzip compressed archive of the fasta files (those ending .fa.gz) and quality scores (those ending .qual.gz) of sequences from the Black samples as supplied by 454, Inc.

Format: ZIP Size: 36.2MB Download file

Open Data

Additional File 1:

Table1SRed. Two lists (one for the Red Sample and one for the Black Sample) describing all the similarities found in the data. The table has the following columns: "Classification I" and "Classification II" are hierarchical classifications of the subsystems. "Subsystem" is the name of the subsystem [25]. "Functional Role" is the role of the protein in the subsystem to which the sequence from the Soudan Mine was similar. "Occurrence" is the number of times that a functional role is found in each sample. The text files have the data as tab separated items, and the file ending .xls has the same data in Microsoft Excel format.

Format: XLS Size: 296KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 2:

Table1SBlack. Two lists (one for the Red Sample and one for the Black Sample) describing all the similarities found in the data. The table has the following columns: "Classification I" and "Classification II" are hierarchical classifications of the subsystems. "Subsystem" is the name of the subsystem [25]. "Functional Role" is the role of the protein in the subsystem to which the sequence from the Soudan Mine was similar. "Occurrence" is the number of times that a functional role is found in each sample. The text files have the data as tab separated items, and the file ending .xls has the same data in Microsoft Excel format.

Format: TXT Size: 186KB Download file

Open Data

Additional File 3:

Table1S. Two lists (one for the Red Sample and one for the Black Sample) describing all the similarities found in the data. The table has the following columns: "Classification I" and "Classification II" are hierarchical classifications of the subsystems. "Subsystem" is the name of the subsystem [25]. "Functional Role" is the role of the protein in the subsystem to which the sequence from the Soudan Mine was similar. "Occurrence" is the number of times that a functional role is found in each sample. The text files have the data as tab separated items, and the file ending .xls has the same data in Microsoft Excel format.

Format: TXT Size: 96KB Download file

Open Data

Additional File 4:

Table2S. The occurrence of subsystems in either the Red Sample or the Black Sample were compared to the subsystems found in the following metagenomes: AMD [7], Farm [6], Whale (all three whale falls combined)[6], the SEED non-redundant database [11], and the Sargasso Sea [10]. For each pair wise comparison the subsystems that are more likely to be found (P > 0.95) in either of the samples are shown, along with the sample that the subsystem is more likely to be found in. Subsystem names and classification are as found at [25]. The text file has the data as tab separated items, and the file ending .xls has the same data in Microsoft Excel format.

Format: XLS Size: 208KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 5:

Table2S. The occurrence of subsystems in either the Red Sample or the Black Sample were compared to the subsystems found in the following metagenomes: AMD [7], Farm [6], Whale (all three whale falls combined)[6], the SEED non-redundant database [11], and the Sargasso Sea [10]. For each pair wise comparison the subsystems that are more likely to be found (P > 0.95) in either of the samples are shown, along with the sample that the subsystem is more likely to be found in. Subsystem names and classification are as found at [25]. The text file has the data as tab separated items, and the file ending .xls has the same data in Microsoft Excel format.

Format: TXT Size: 73KB Download file

Open Data