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Erin Jones

Brigham Young University | Graduate student

Subject Areas: Water quality, aquatic microbial ecology

 Recent activity

ABSTRACT:

This dataset includes R code, specifically the package WaterML, to download water quality data from iUTAH GAMUT station sensors installed to look at water quality/quantity along three montane-to-urban watersheds: Logan River, Red Butte Creek, and Provo River. An explanation of the GAMUT sensor network can be found at gamut.iutahepscor.org. The code requires installation of packages 'plyr' and 'WaterML'. Instructions for modifying code to extract sensor data for your timepoint of interest are included in the README file. The code has the option to write sensor data to .csv files in your working directory.

Additional code available at https://github.com/erinfjones/GAMUTdownload

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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.

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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ABSTRACT:

This dataset contains a .biom file of OTU (operational taxonomic units) classifications for eukaryotes at iUTAH GAMUT sites in three watersheds in May of 2015. Briefly, water column samples were filtered on 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits. We sequenced 18S region amplicons using Illumina Hi-Seq and then a modified MOTHUR protocol (Silva v. 132 reference file, command codes in mothureukaryotes.txt) to generate OTU classifications. Sample metadata (including site information and sample chemistry from grab samples or sensor data) is in design.csv.

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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.

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ABSTRACT:

This dataset includes sub-watershed delineations created for ~66 stream sites across the three iUTAH GAMUT watersheds, Logan River, Red Butte Creek, and Provo River (including GAMUT Aquatic stations: gamut.iutahepscor.org ), where monthly water quality samples were collected 2013-2014. Sub-watershed delineations will allow for analysis of the landscape contributing to these sites, which can then be used in models of water quality for the stream sites. This will contribute to the iUTAH goal of modeling the impact of land-use changes on in-stream water quality.

Delineations were generated from 10 m DEMs (Utah GIS portal) using ArcMap tools: mosiac, fill, flow direction, flow accumulation, snap pour point, watershed and raster to polygon. Default settings were used for all tools.

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 Contact

Resources
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Collection 0
Composite Resource 0
Generic 0
Geographic Feature 0
Geographic Raster 0
HIS Referenced Time Series 0
Model Instance 0
Model Program 0
MODFLOW Model Instance Resource 0
Multidimensional (NetCDF) 0
Script Resource 0
SWAT Model Instance 0
Time Series 0
Web App 0
Generic Generic
Wasatch Range Metropolitan Area E. coli densities
Created: Sept. 10, 2015, 8:40 p.m.
Authors: Erin Jones

ABSTRACT:

E. coli densities measured in 3 Wasatch Range Metropolitan Area watersheds: Logan, Red Butte and Provo for 1 year.

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Generic Generic

ABSTRACT:

This dataset includes sub-watershed delineations created for ~66 stream sites across the three iUTAH GAMUT watersheds, Logan River, Red Butte Creek, and Provo River (including GAMUT Aquatic stations: gamut.iutahepscor.org ), where monthly water quality samples were collected 2013-2014. Sub-watershed delineations will allow for analysis of the landscape contributing to these sites, which can then be used in models of water quality for the stream sites. This will contribute to the iUTAH goal of modeling the impact of land-use changes on in-stream water quality.

Delineations were generated from 10 m DEMs (Utah GIS portal) using ArcMap tools: mosiac, fill, flow direction, flow accumulation, snap pour point, watershed and raster to polygon. Default settings were used for all tools.

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Generic Generic
Aquatic GAMUT Bacterial Community Target Metagenomics-454 Pyro
Created: July 27, 2016, 12:36 a.m.
Authors: Erin Jones · Zach Aanderud

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.

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Generic Generic
Aquatic GAMUT Eukaryote Metagenomics
Created: July 31, 2017, 6:10 p.m.
Authors: Erin Jones · Zach Aanderud

ABSTRACT:

This dataset contains a .biom file of OTU (operational taxonomic units) classifications for eukaryotes at iUTAH GAMUT sites in three watersheds in May of 2015. Briefly, water column samples were filtered on 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits. We sequenced 18S region amplicons using Illumina Hi-Seq and then a modified MOTHUR protocol (Silva v. 132 reference file, command codes in mothureukaryotes.txt) to generate OTU classifications. Sample metadata (including site information and sample chemistry from grab samples or sensor data) is in design.csv.

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Generic Generic
Aquatic GAMUT Bacterial Community Target Metagenomics-HiSeq
Created: July 31, 2017, 6:30 p.m.
Authors: Erin Jones · Zach Aanderud

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.

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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Composite Resource Composite Resource
Aquatic GAMUT sensor data download (WaterML in R)
Created: Jan. 2, 2018, 8:38 p.m.
Authors: Erin Jones

ABSTRACT:

This dataset includes R code, specifically the package WaterML, to download water quality data from iUTAH GAMUT station sensors installed to look at water quality/quantity along three montane-to-urban watersheds: Logan River, Red Butte Creek, and Provo River. An explanation of the GAMUT sensor network can be found at gamut.iutahepscor.org. The code requires installation of packages 'plyr' and 'WaterML'. Instructions for modifying code to extract sensor data for your timepoint of interest are included in the README file. The code has the option to write sensor data to .csv files in your working directory.

Additional code available at https://github.com/erinfjones/GAMUTdownload

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