genetics

Descriptive data file for information regarding microbial genetic research in the environs of Plum Island Sound watersheds, PIE LTER, Massachusetts.

Abstract: 

This is a descriptive, tabular dataset of publications related to microbial or genomic research conducted within PIE.   Assession numbers for genetic sequences  generated from PIE samples are provided where available, followed by a very brief description of analysis type and study objectives.  Sampling  locations within PIE, sampling dates,  and habitat type (sea water, fresh water, sediment, marsh) are also given.   Environmental data are included in some publications and are listed here (if brief) or availability is described.    Links to sequence archives are given in Methods.

Core Areas: 

Data set ID: 

222

Keywords: 

Short name: 

PIE-Microbe-Genomics

Purpose: 

 

Data sources: 

PIE-Microbe-Genomics.xls

Methods: 

Microbial genomic sequence data is available by conducting searches using accession numbers associated with  the sequence of interest.

Examples of of searches are:
Entrez search, easily search by single accession number; returns sequence and publication information.  Link: http://www.ncbi.nlm.nih.gov/sites/gquery
Batch Entrez, Batch search a series of accession numbers after creating a Fasta-formatted text file;  returns links to GenBank, Fasta, Graphics, Population Set and Related Sequences for each accession number.
Link: http://ncbi.nlm.nih.gov/sites/batchentrez

Batch Entrez Fasta-formatted text file should be a  single column list of accession numbers with a ".1" added like a file extension. File should have no header line. Go to http://ncbi.nlm.nih.gov/sites/batchentrez, follow the web site directions for  using Batch Entrez

Fasta-formatted text file example:
AY836800.1
AY836801.1
AY836802.1
AY836803.1
etc..

To access  MG-RAST annotation and raw sequences, the user will need to navigate to this page:
http://www.mg-rast.org/mgmain.html?mgpage=search
and enter the project id listed in the PIE-Microbe-Genomics tab (e.g. mgp84173) into the text box at the upper left of the page adjacent to the "search" button. 
The search will return a list of the samples associated with the project and a link to download the annotation, fasta files, and associated metadata.

Data can also be accessed through the API according to the instructions here
http://api-ui.mg-rast.org/api.html

Also available, courtesy of Joe Vineis, is a small git repository that includes some simple instructions for handling the API for beginners:
https://github.com/jvineis/mg_rast_processing

 

Maintenance: 

Ongoing research

Version 01: March 6, 2012, updated data and metadata. Used MarcrosExportEML_HTML (working)pie_excel2007.xlsm 2/28/2012 8:18 PM for QA/QC to EML 2.1.0

Version 02: April 20, 2018, data and metadata created to comply with importation to Drupal and LTER PASTA. Used MarcrosExportEML_HTML (working)pie_excel2007_Jan2018.xlsm 1/30/2018 2:24 PM for QA/QC to EML 2.1.0

Version 03: August 13, 2019, edited URL made shorter, data and metadata updates to comply with importation to DEIMS7 and LTER Data Portal. Used MarcrosExportEML_HTML (working)pie_excel2007_Jun2019.xlsm 6/7/19 12:58 PM for QA/QC to EML 2.1.0.

Version 04: August 26, 2019, data and metadata updates to comply with importation to DEIMS7 and LTER Data Portal. Used MarcrosExportEML_HTML (working)pie_excel2007_Jun2019.xlsm 6/7/19 12:58 PM for QA/QC to EML 2.1.0

 

Additional information: 

 

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