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Aquatic GAMUT Bacterial Community Target Metagenomics-454 Pyro


Authors: Erin Jones Zach Aanderud
Owners: iUTAH Data Manager Erin Jones
Resource type: Generic
Storage: The size of this resource is 1.4 MB
Created: Jul 27, 2016 at 12:36 a.m.
Last updated: Jan 02, 2018 at 8:20 p.m. by Erin Jones
Citation: See how to cite this resource
Sharing Status: Public
Views: 110
Downloads: 6
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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 in September 2014. Briefly, water column samples were filtered onto 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits. We sequenced bacterial DNA (PCR-amplified using V4-region specific primers) using 454-pyrosequencing (an older sequencing method with more limitations). We cleaned, clustered (using 97% OTU similarity cut-off) and aligned sequences using the Schloss 2011 protocol, and classified OTUs to taxonomy based on the SILVA bacteria database. Code used for analysis 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.

Schloss PD, Gevers D, Westcott SL. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS ONE. 6:e27310.

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).

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 (2018). Aquatic GAMUT Bacterial Community Target Metagenomics-454 Pyro, HydroShare, http://www.hydroshare.org/resource/48fc6871c51d436b83000a8d29ddb702

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

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

Comments

Erin Jones 1 year, 9 months ago

Illumina Hi-Seq samples from September 2014-October 2015 are also available on HydroShare.

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