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Aquatic GAMUT Bacterial Community Target Metagenomics-HiSeq


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Resource type: Generic
Storage: The size of this resource is 874.6 MB
Created: Jul 31, 2017 at 6:30 p.m.
Last updated: Aug 13, 2019 at 10:31 p.m.
DOI: 10.4211/hs.c0a1bb39015444ef86ace38ae6c44e77
Citation: See how to cite this resource
Sharing Status: Published
Views: 399
Downloads: 35
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Abstract

This data was collected as part of a study to understand the connectivity and diversity of stream bacteria communities in streams flowing from high to low elevation through different types of urbanization and in different seasons. The dataset contains OTU (operational taxonomic units, the bacterial surrogate for species) abundance for bacteria at iUTAH aquatic GAMUT sites (http://data.iutahepscor.org/mdf/Data/Gamut_Network/) in three watersheds at 3 time points (November 2014, February 2015, and May 2015). Briefly, we filtered water column samples onto 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits (alternate low protocol yield using phenol chloroform). We sequenced bacterial DNA (PCR-amplified using V4 region specific primers) using Illumina Hi-Seq. We cleaned, clustered (using 97% OTU similarity cut-off) and aligned sequences using the Kozich et al. 2013 protocol, and classified OTUs to taxonomy based on the SILVA bacteria database. Code used for processing is available at https://github.com/erinfjones/mothurcode.

There are three files; site and sample metadata (e.g. date sampled) is included in the file stream_design.txt, observed OTU counts by sample are in the .shared file, and the taxonomic classification of OTUs is in the .taxonomy file.

Also included are zipped folders containing raw fastq files.

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013): Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology. 79(17):5112-20.

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Resource Level Coverage

Spatial

Coordinate System/Geographic Projection:
WGS 84 EPSG:4326
Coordinate Units:
Decimal degrees
Place/Area Name:
Multiple Watersheds
North Latitude
41.9615°
East Longitude
-110.8809°
South Latitude
40.4010°
West Longitude
-111.9795°

Temporal

Start Date:
End Date:

Content

Additional Metadata

Name Value
Observed Variables Rank abundance
Variable Description Relative abundance of bacterial community taxa in water column
Data Processing Method Sequences have been processed using MOTHUR (Schloss et al. 2009).
Data Collection Method Streamwater aseptically vacuum filtered in the field or lab using autoclaved Nalgene filter cups and 47 mm 0.2 um membrane filters, were stored on dry ice or liquid nitrogen until extracted with MoBIO PowerMax Soil DNA kits. PCR-amplified 16S rDNA samples were sequenced using BYU’s DNA Sequencing Center (454-Pyrosequencing or Hi-Seq).

References

Credits

Funding Agencies

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
National Science Foundation iUTAH-innovative Urban Transitions and Aridregion Hydro-sustainability 1208732

How to Cite

Jones, E., Z. Aanderud (2019). Aquatic GAMUT Bacterial Community Target Metagenomics-HiSeq, HydroShare, https://doi.org/10.4211/hs.c0a1bb39015444ef86ace38ae6c44e77

This resource is shared under the Creative Commons Attribution CC BY.

 http://creativecommons.org/licenses/by/4.0/
CC-BY

Comments

Erin Jones 2 years, 4 months ago

454-pyrosequence of September samples are also available on HydroShare.

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