http://lod.bco-dmo.org/id/dataset/754623
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2019-02-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accession numbers and associated metadata for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals
2019-02-04
publication
2019-02-04
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-03-18
publication
https://doi.org/10.26008/1912/bco-dmo.754623.1
Stephen R. Palumbi
Stanford University - Hopkins
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Palumbi, S. R. (2022) NCBI accession numbers and associated metadata for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-02-04 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.754623.1 [access date]
Accession numbers for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals Dataset Description: <p>Raw low-coverage genomic sequence reads:&nbsp;1190 files with raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals (some individuals are represented by multiple sequence data files) are deposited in the NCBI Sequence Read Archive (SRA) with accession numbers SRS2001281- SRS2003099 associated with BioProject PRJNA376564 and BioSamples SAMN06436077 - SAMN06436952.</p> Methods and Sampling: <p>Species: Atlantic silverside (<em>Menidia menidia)</em><br />
Source: From laboratory breeding experiment or wild caught at one of four locations along the east coast of North America.<br />
Library preparation method: Modified version of Illumina Nextera sample preparation kit.<br />
Sequencing instrument: Illumina HiSeq 2000<br />
Read type: Paired-end 125 bp<br />
Sequencing strategy: Whole genome sequencing</p>
<p>The sequence data were prepared as described in Therkildsen &amp; Palumbi (2017).</p>
<p>The tissue samples used for sequencing had been stored in minus 20 degrees C freezer for 8-17 years prior to DNA extraction. We used the Qiagen DNeasy Blood and Tissue kit to extract DNA from muscle tissue and evaluated the degradation level of each extract through 1.5% agarose gel electrophoresis. Only samples that showed clear high molecular weight bands and limited smearing were retained for library preparation. To ensure DNA integrity in the retained samples, we removed fragments shorter than ~1000 bp from each extract using Agencourt AMPure XP beads in a 0.4:1 AMPure to sample ratio and eluted the DNA in 10 mM Tris-Cl, pH 8.5.</p>
<p>We measured DNA concentrations with a Quant-iT high-sensitivity assay (Invitrogen) and prepared a separate barcoded library for each individual with Illumina’s Nextera kit according to the protocol described in Therkildsen and Palumbi (2017). Briefly, the tagmentation reaction, which simultaneously fragments the DNA and incorporates partial adapters, was carried out in a 2.5 ul volume with 1.6–7.9 ng of input DNA for each library. We then used a two-step PCR procedure with a total of 12 cycles (8 + 4) to add the remaining Illumina adapter sequence with dual index barcodes and amplify the libraries. The PCR was conducted with the KAPA Library Amplification Kit and the Illumina Nextera index kit with primers N501– N508 + S511 and N701–N712 + N714. As a final step, we purified and size-selected the amplification products with Agencourt AMPure XP beads and quantified the concentration of the final libraries with the Invitrogen Quant-iT high-sensitivity assay. We also examined the fragment size distribution of multiple libraries from each plate on an Agilent Bioanalyzer instrument.</p>
<p>We combined equimolar amounts of 56–76 libraries into separate pools for sequencing across 13.5 lanes of paired-end 125-bp reads on an Illumina HiSeq 2000 (v4 chemistry) at the University of Utah’s Bioinformatics Core Facility. To even out the data yield among samples, we repooled libraries that initially had obtained the lowest read output for supplementary sequencing in 4.5 additional HiSeq lanes.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1434325 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1434325
completed
Stephen R. Palumbi
Stanford University - Hopkins
831-655-6214
Hopkins Marine Station 120 Ocean View Blvd
Pacific Grove
CA
93950
USA
spalumbi@stanford.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioSample_Accession
BioProject_Accession
SRA_Accession
Species
Sample_ID
Breed
Collection_Site
Latitude
Longitude
Collection_Year
Illumina HiSeq 2000
theme
None, User defined
accession number
species scientific name (binomial)
sample identification
sample description
site
latitude
longitude
year
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
Palumbi_silversides
service
Deployment Activity
NY, GA, Nova Scotia, & Quebec
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
High resolution genome changes during evolution in a classic fisheries experiment
https://osprey.bco-dmo.org/project/516279
High resolution genome changes during evolution in a classic fisheries experiment
<p><em>Description from NSF award abstract:</em><br />
One of the strongest impacts there is on ocean species is reduction in population size due to fishing. Even for species that are not overfished, harvest takes a large fraction of the biggest and fastest growing individuals. As a result, fishing exerts strong natural selection on fish population, selecting for slow growing, small individuals. Experiments in artificial fishing have shown rapid evolution of growth rates, maturation size and other traits for lab populations. The classic Conover-Munsch experiments ten years ago showed the power of fishing to generate rapid evolution. However, no analysis of the genetic impact of fishing under such controlled conditions has been done, and no investigation of the way whole genomes respond to strong fisheries evolution has been attempted. Luckily, the Conover-Munsch samples - from the fish used in their classic experiment - have been preserved, and modern genomic techniques are now available that can analyze the way fisheries-induced evolution shaped the genetic diversity and genome architecture of these populations. Strong selection is known in other systems to leave a legacy of deleterious changes in the genome. The results of this study will be important components of understanding the long-term effects of fishing because they will for the first time allow a mechanistic understanding of how natural selection works on fish populations. The project will also compare the changes that occur after the relaxation of fishing pressure to estimate if there is a legacy of deleterious genome changes in fished species that impedes their recovery. The data from this study will show how fishing creates change at loci under selection, and also how this strong selection generates other, non-adaptive shifts because of genetic hitchhiking and inbreeding.</p>
<p>The investigators will use next generation DNA sequencing to sequence the protein coding regions of the Conover-Munsch fish samples. They will discover, document and compare genetic variants across the genome in lines selected for large size, in lines selected for small size, and in the original populations in order to chart evolutionary changes at the genomic level imposed by fishing. They will use outlier analyses to pinpoint loci at which strong selection has acted to change allele frequencies. They will compare these changes to changes in fish populations after the relaxation of fishing in order to distinguish evolutionary changes that are easily reversible from those that are not. In addition, they will also compare genetic changes induced by fishing to those that occur naturally along an environmental gradient on the US east coast. Preliminary data indicate that many of the genetic variants selected for in the fisheries experiment are old variants - estimated by patterns of linkage disequilibrium - already present in the original population. Working on the genetics of the natural gradient will show which of these variants have been selected by evolutionary forces in the native environment, and subsequently been favored by the novel evolutionary pressure of fishing.</p>
Fishery Genome Changes
largerWorkCitation
project
eng; USA
oceans
NY, GA, Nova Scotia, & Quebec
-81.43
-61.85
31.02
47.4
1998-01-01
2007-12-31
The East coast of North America
0
BCO-DMO catalogue of parameters from NCBI accession numbers and associated metadata for raw low-coverage genomic sequence reads from 876 different Atlantic silverside individuals
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/754634.rdf
Name: BioSample_Accession
Units: unitless
Description: <p>NCBI BioSample Accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/754635.rdf
Name: BioProject_Accession
Units: unitless
Description: <p>NCBI BioProject Accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/754636.rdf
Name: SRA_Accession
Units: unitless
Description: <p>NCBI SRA Accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/754637.rdf
Name: Species
Units: unitless
Description: <p>Species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/754638.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/754639.rdf
Name: Breed
Units: unitless
Description: <p>Laboratory breed or wild caught</p>
http://lod.bco-dmo.org/id/dataset-parameter/754640.rdf
Name: Collection_Site
Units: unitless
Description: <p>Collection site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/754833.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of collection site; positive values = North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/754834.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of collection site; positive values = East.</p>
http://lod.bco-dmo.org/id/dataset-parameter/871699.rdf
Name: Collection_Year
Units: unitless
Description: <p>Year of collection (YYYY)</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
97892
https://darchive.mblwhoilibrary.org/bitstream/1912/28213/1/dataset-754623_atlantic-silverside-menidia-menidia-raw-low-coverage-genomic-sequence-accessions__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.754623.1
download
onLine
dataset
<p>Species: Atlantic silverside (<em>Menidia menidia)</em><br />
Source: From laboratory breeding experiment or wild caught at one of four locations along the east coast of North America.<br />
Library preparation method: Modified version of Illumina Nextera sample preparation kit.<br />
Sequencing instrument: Illumina HiSeq 2000<br />
Read type: Paired-end 125 bp<br />
Sequencing strategy: Whole genome sequencing</p>
<p>The sequence data were prepared as described in Therkildsen &amp; Palumbi (2017).</p>
<p>The tissue samples used for sequencing had been stored in minus 20 degrees C freezer for 8-17 years prior to DNA extraction. We used the Qiagen DNeasy Blood and Tissue kit to extract DNA from muscle tissue and evaluated the degradation level of each extract through 1.5% agarose gel electrophoresis. Only samples that showed clear high molecular weight bands and limited smearing were retained for library preparation. To ensure DNA integrity in the retained samples, we removed fragments shorter than ~1000 bp from each extract using Agencourt AMPure XP beads in a 0.4:1 AMPure to sample ratio and eluted the DNA in 10 mM Tris-Cl, pH 8.5.</p>
<p>We measured DNA concentrations with a Quant-iT high-sensitivity assay (Invitrogen) and prepared a separate barcoded library for each individual with Illumina’s Nextera kit according to the protocol described in Therkildsen and Palumbi (2017). Briefly, the tagmentation reaction, which simultaneously fragments the DNA and incorporates partial adapters, was carried out in a 2.5 ul volume with 1.6–7.9 ng of input DNA for each library. We then used a two-step PCR procedure with a total of 12 cycles (8 + 4) to add the remaining Illumina adapter sequence with dual index barcodes and amplify the libraries. The PCR was conducted with the KAPA Library Amplification Kit and the Illumina Nextera index kit with primers N501– N508 + S511 and N701–N712 + N714. As a final step, we purified and size-selected the amplification products with Agencourt AMPure XP beads and quantified the concentration of the final libraries with the Invitrogen Quant-iT high-sensitivity assay. We also examined the fragment size distribution of multiple libraries from each plate on an Agilent Bioanalyzer instrument.</p>
<p>We combined equimolar amounts of 56–76 libraries into separate pools for sequencing across 13.5 lanes of paired-end 125-bp reads on an Illumina HiSeq 2000 (v4 chemistry) at the University of Utah’s Bioinformatics Core Facility. To even out the data yield among samples, we repooled libraries that initially had obtained the lowest read output for supplementary sequencing in 4.5 additional HiSeq lanes.</p>
Specified by the Principal Investigator(s)
<p>The following samples should be excluded from analysis because of possible errors during library preparation:<br />
D1Gen10_1496<br />
D1Gen10_748<br />
D1Gen10_749<br />
D1Gen10_755<br />
D1Gen10_767<br />
D1Gen10_774<br />
D1Gen10_776<br />
D1Gen10_778<br />
D1Gen10_780<br />
D1Gen5_250<br />
D1Gen5_332<br />
D2Gen10_425<br />
D2Gen10_445<br />
JekyllIs_1223<br />
JekyllIs_1224<br />
MagdalenIs_911<br />
MagdalenIs_912<br />
MagdalenIs_913<br />
MagdalenIs_914<br />
MagdalenIs_915<br />
MagdalenIs_916<br />
MagdalenIs_917<br />
MagdalenIs_918<br />
Patchogue_1030<br />
R1Gen5_1357<br />
RGen0_701<br />
U2Gen10_1199<br />
U2Gen10_1200<br />
U2Gen10_1201<br />
U2Gen10_1479</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina HiSeq 2000
Illumina HiSeq 2000
PI Supplied Instrument Name: Illumina HiSeq 2000 Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Deployment: Palumbi_silversides
Palumbi_silversides
Poquott Beach
shoreside
Palumbi_silversides
Stephen R. Palumbi
Stanford University
Poquott Beach
shoreside