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This resource does not have an owner who is an active HydroShare user. Contact CUAHSI (help@cuahsi.org) for information on this resource. |
| Type: | Resource | |
| 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. | |
| Citation: | See how to cite this resource |
| Sharing Status: | Public |
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| Views: | 2413 |
| Downloads: | 46 |
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| Comments: | 1 comment |
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.
Subject Keywords
Coverage
Spatial
Temporal
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Content
Additional Metadata
| Name | Value |
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| Observed Variables | Rank abundance |
| Variable Description | Relative abundance of bacterial community taxa in water column |
| 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). |
| Data Processing Method | Sequences have been processed using MOTHUR (Schloss et al. 2009). |
Credits
Funding Agencies
This resource was created using funding from the following sources:
| Agency Name | Award Title | Award Number |
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| National Science Foundation | iUTAH-innovative Urban Transitions and Aridregion Hydro-sustainability | 1208732 |
How to Cite
This resource is shared under the Creative Commons Attribution CC BY.
http://creativecommons.org/licenses/by/4.0/
Comments
Erin Fleming Jones 7 years, 3 months ago
Illumina Hi-Seq samples from September 2014-October 2015 are also available on HydroShare.
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