Dataset: Raw low-coverage whole genome sequencing reads

Name: Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007
Published: 2021-06-30
Keywords: Local adaptation, Whole Genome Sequencing, Atlantic silversides, genomic differentiation, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:47.4 E:-61.85 S:31.02 W:-81.43

Temporal Extent: 2005 - 2007

Project:

Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline (GenomAdapt)

Principal Investigator:

Nina Overgaard Therkildsen (Cornell University, Cornell)

Co-Principal Investigator:

Hannes Baumann (University of Connecticut, UConn)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-06-30

Restricted:

Validated:

Current State:

Preliminary and in progress

Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007

Abstract:

Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside individuals (some individuals are represented by multiple sequence data files). The raw low-coverage genomic sequence reads are deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA376564. These data were published in Wilder et al. (2020).

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Methods & Sampling

The following is an excerpt of the methods used to generate these data. Full details can be found in the associated publication and supplemental material of Wilder et al. (2020).

Data generation:

Atlantic silverside muscle samples collected from Georgia (GA), New York (NY), Gulf of Maine (GoM) and Gulf of St. Lawrence (GSL) were sequenced by Therkildsen & Palumbi (2017) to a final, average depth of 1.5x across the reference transcriptome. All the samples were collected in the spring. See Therkildsen & Palumbi (2017) and Therkildsen et al. (2019) for further detail. We added 47 additional samples from Oregon Inlet, North Carolina (NC) near Cape Hatteras.

Individually barcoded sample libraries were prepared at Cornells Biotechnology Resource Center using similar methods to Therkildsen & Palumbi (2017), with a few minor modifications. Reagents from the Illumina Nextera kit (96 sample Nextera DNA Library Prep Kit) were used at 1/3 the recommended concentration in 1/10 the recommended volume (5ul instead of 50ul), with 2ng of input DNA. Individual libraries were pooled, and size-selected using a Pippin Prep to remove fragments <286 bp (150 bp insert plus 136 bp of Illumina adapters). Filtered mapped reads for the NC samples had a final average depth of 1.5x.

Sampling and analytical procedures:

Samples were collected directly from the wild as described in Hice et al. (2012).

Locations:
Five locations along the east coast of North America.

USA:Jekyll Island,Georgia 31.02 -81.43
USA:Oregon Inlet,NorthCarolina 35.77 -75.52
USA:Minas Basin,Gulf of Maine 45.2 -64.38
USA:Patchogue,NewYork 40.75 -73.00
Canada:Magdalen Island, Gulf of St. Lawrence 47.4 -61.85

Problem report:

The following samples should be excluded from analysis because of possible errors during library preparation:
JekyllIs_1223, JekyllIs_1224, MagdalenIs_911, MagdalenIs_912, MagdalenIs_913, MagdalenIs_914, MagdalenIs_915, MagdalenIs_916, MagdalenIs_917, MagdalenIs_918, Patchogue_1030

Data Processing Description

BCO-DMO Data Manager Processing Notes:
* Converted SampleLocationDetails.xlsx Sheet 1 to csv and imported into the BCO-DMO data system.
* Split latitude and longitude into respective columns from combined string column.
* replaced comma in geolocation name to semicolon for better support for csv exports.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1756316
NSF Division of Ocean Sciences	OCE-1756751

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2000

Supplied Description:

Illumina HiSeq 2000 with paired-end 125 bp (for samples from GA, NY, GoM, and GSL)

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Automated DNA Sequencer

Supplied Name: Illumina NextSeq500

Supplied Description:

Illumina NextSeq500 paired-end 75 bp (for samples from NC)

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
SampleID	Sample identifier	unitless	sample
bioproject_accession	NCBI BioProject accession number	unitless	BioProject
biosample_accession	NCBI BioSample accession number	unitless	BioSample
Population	Description of the population sampled by region name	unitless	site
collection_date	Collection year in format yyyy	unitless	year
geo_loc_name	Geolocation name of the collection	unitless	site
lat	Collection latitude	decimal degrees	lat
lon	Collection longitude	decimal degrees	lon

Database

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Dataset: Raw low-coverage whole genome sequencing reads