http://lod.bco-dmo.org/id/dataset/883426
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
2022-11-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Evolutionary and acclimatory shifts in gene expression of Eurytemora affinis copepods reared in saline and freshwater conditions during laboratory experiments from 2011-2014
2022-11-10
publication
2022-11-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-11-12
publication
https://doi.org/10.26008/1912/bco-dmo.883426.1
Carol E. Lee
University of Wisconsin
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: Posavi, M., Lee, C. E. (2022) Evolutionary and acclimatory shifts in gene expression of Eurytemora affinis copepods reared in saline and freshwater conditions during laboratory experiments from 2011-2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-11-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.883426.1 [access date]
Methods and Sampling: <p><strong>Study objectives</strong><br />
The goal of this study was to explore evolutionary shifts in gene expression between ancestral saline and freshwater invading populations of the <em>Eurytemora affinis</em>&nbsp;(copepod) species complex on a genome-wide scale.&nbsp;</p>
<p>To explore mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, laboratory experiments were conducted using both ancestral saline and derived freshwater populations of <em>Eurytemora affinis</em>.&nbsp;&nbsp;Then&nbsp;<span style="background-color:rgb(255, 255, 255); color:rgb(51, 51, 51); font-family:sans-serif,arial,verdana,trebuchet ms; font-size:13px">RNA-seq data -- Illumina short paired-end (PE) reads (101 base pairs) of 10 freshwater and 12 saline&nbsp;</span><em>E.affinis</em><span style="background-color:rgb(255, 255, 255); color:rgb(51, 51, 51); font-family:sans-serif,arial,verdana,trebuchet ms; font-size:13px">&nbsp;samples --&nbsp;</span>were used to answer the following questions:</p>
<ul>
<li>(1)&nbsp; What are the patterns of evolutionary shifts in gene expression between the ancestral saline and freshwater invading populations?</li>
<li>(2)&nbsp; What are the plastic (acclimatory) changes in gene expression between salinities (0 PSU vs. 15 PSU conditions) within each of the saline and freshwater populations?</li>
<li>(3)&nbsp; Are the magnitude and direction of plasticity in gene expression correlated with evolutionary responses?</li>
<li>(4)&nbsp; Has plasticity in gene expression evolved following freshwater invasions?</li>
</ul>
<p><strong>Collection of ancestral populations</strong><br />
The copepods were collected using a plankton net mesh size&nbsp;of 50 μm&nbsp;in diameter, from a depth of 1-4 meters from near the shore.&nbsp;The freshwater copepods were collected in April-May 2006 by throwing the plankton net off the dock in Racine Harbor, Lake Michigan in Wisconsin, USA (42.729444 N, 87.778889 W). The saline copepods were collected by small boats near the shore in Baie de L'Isle Verte, St. Lawrence marsh, Quebec, Canada (48.003889 N, 69.425278 W)&nbsp;in May-June 2006.&nbsp; Collected samples were transported to the laboratory where&nbsp;<em>Eurytemora affinis</em>&nbsp;individuals were identified and sampled under the microscope.</p>
<p><strong>Laboratory cultures and experiments</strong><br />
Four inbred lines of <em>Eurytemora affinis</em>&nbsp;(two each from the two populations) were generated&nbsp;through full-sibling mating for 30 generations. Two independent saltwater inbred lines (SW1 and SW2) were derived from the ancestral saline population in Baie de L’Isle Verte (Canada) and reared at their native salinity of 15 PSU.&nbsp; The&nbsp;two freshwater inbred lines (FW1 and FW2)&nbsp;were derived from the freshwater invading population in Racine Harbor (USA) and reared in Lake Michigan water (0 PSU, conductivity 300&nbsp;μS/cm). In addition, reciprocal F1 crosses between freshwater and saline inbred lines were created and reared to test for allele-specific expression by comparing gene expression in parental lines and their F1 crosses.</p>
<p>Two replicate common-garden reaction norm experiments, each consisting of a 2 × 2 factorial design, were performed to compare patterns of the gene expression of the FW and SW inbred lines (see Materials and Methods in Posavi et al. 2020).&nbsp; Total RNA from whole bodies of 50 copepods (25 females and 25 males) per sample was extracted using Trizol reagent (Ambion RNA) and Qiagen RNeasy Mini Kit for purification (Qiagen cat. no. 74104). Extracted and purified RNA samples were stored at -80 degrees Celsius until sequencing. The strand-specific Illumina RNA-seq libraries (Parkhomchuk et al., 2009) of polyA purified mRNA were constructed using the TruSeq RNA Sample Prep kit (Illumina). Three biological replicates per inbred line were sequenced using the Illumina HiSeq 2000 platform in the Institute for Genome Sciences at the University of Maryland School of Medicine and generated 101-bp-long paired-end read data.&nbsp;</p>
<p>These data have important implications for understanding&nbsp;the evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats.&nbsp;</p>
<p><strong>Problem report</strong><br />
One replicate of the FW1 inbred line was excluded because of bacterial infection</p>
<p><strong>Additional information</strong><br />
~ Detailed methods, results, and figures can be found in Posavi et al. (2020) (<em>see Related Publications section</em>).&nbsp;<br />
~ The sequence data can be viewed under NCBI BioProject PRJNA278152 (<em>see Related Datasets</em>).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658517 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658517
completed
Carol E. Lee
University of Wisconsin
Department of Integrative BIology, Birge Hall 430 Lincoln Drive
Madison
WI
53706
USA
carollee@wisc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Record_num
Culture_sample_date
Sample_name
Organism
Sex
Female_inbred_line
female_ancestor_location
Male_inbred_line
male_ancestor_location
Experimental_culture
Description
Salinity_conditions_rearing
PSU_culture
BioProject
SRA
BioSample
Illumina HiSeq 2000
theme
None, User defined
sampling_sequence
date
sample identification
sample description
site description
experiment id
experiment type
treatment
salinity
NCBI BioProject accession
NCBI SRA Sample accession (SRS)
NCBI BioSample accession
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Plankton Net
instrument
BCO-DMO Standard Instruments
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.
Evolutionary Responses to Global Changes in Salinity and Temperature
https://osprey.bco-dmo.org/project/816918
Evolutionary Responses to Global Changes in Salinity and Temperature
<p>NSF Award Abstract:</p>
<p>Drastic changes in the global water cycle and increases in ice melt are causing the freshening of Northern coastal seas. The combination of both reduced salinity and increased temperature will likely act in concert to reduce populations of estuarine and marine organisms. Data indicate that reduced salinity and high temperature would each increase the energy costs as well as reduce survival and reproduction of the common copepod Eurytemora affinis. This project will examine the joint effects of salinity reduction and temperature increase on the evolutionary responses of populations of E. affinis in the wild, as well as in selection experiments in the laboratory. This study will provide novel insights into responses of organisms to climate change, as no study has analyzed the joint impacts of salinity and temperature on evolutionary responses, and relatively few studies have examined the impacts of declining salinity. In general, how selection acts at the whole genome level is not well understood, particularly for non-model organisms. As a dominant estuarine copepod, E. affinis is among the most important species sustaining coastal food webs and fisheries in the Northern Hemisphere, such as salmon, herring, and anchovy. Thus, insights into its evolutionary responses with changing climate have important implications for sustainability of fisheries and food security. Two graduate students from historically underrepresented groups will be trained during this project. The project will have additional societal benefits, including development of educational modules for K-12 students and international collaboration.</p>
<p>This study will address the following questions: (1) To what extent could populations evolve in response to salinity and temperature change, and what are the fitness and physiological costs? (2) How will populations respond to the impacts of salinity-temperature interactions? (3) Do wild populations show evidence of natural selection in response to salinity and temperature? To analyze the evolutionary responses of E. affinis populations to the coupled impacts of salinity and temperature, the investigator will perform laboratory selection experiments and population genomic surveys of wild populations. Selection experiments constitute powerful tools for determining the rate, trajectory, and limits of adaptation. During laboratory selection, evolutionary shifts in fitness-related traits and genomic expression will be examined, as well as genomic signatures of selection in response to low salinity and high temperature selection regimes. The investigator will also conduct population genomic sequencing of E. affinis populations that reside along salinity and temperature gradients in the St. Lawrence and Baltic Sea, and identify genes that show signatures of selection. The project will determine whether the loci that show signatures of selection in the wild populations are the same as those favored during laboratory selection. This reproducibility will provide greater confidence that the genes involved in adaptation to salinity and/or temperature have been captured.</p>
Evolutionary genomics of a copepod
largerWorkCitation
project
eng; USA
biota
oceans
-87.778889
-69.425278
42.729444
48.003889
2011-09-28
2014-03-18
St. Lawrence estuary, Gulf of Mexico, Great Lakes, Baltic Sea
0
BCO-DMO catalogue of parameters from Evolutionary and acclimatory shifts in gene expression of Eurytemora affinis copepods reared in saline and freshwater conditions during laboratory experiments from 2011-2014
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/883631.rdf
Name: Record_num
Units: unitless
Description: <p>Record number</p>
http://lod.bco-dmo.org/id/dataset-parameter/883632.rdf
Name: Culture_sample_date
Units: unitless
Description: <p>Date of sampling for the inbred line and F1 crosses</p>
http://lod.bco-dmo.org/id/dataset-parameter/883633.rdf
Name: Sample_name
Units: unitless
Description: <p>Sample name indicating the E.affinis line, salinity PSU, and replicate number</p>
http://lod.bco-dmo.org/id/dataset-parameter/883634.rdf
Name: Organism
Units: unitless
Description: <p>Organism that was raised and studied (copepod Eurytemora affinis)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883635.rdf
Name: Sex
Units: unitless
Description: <p>Sex of copepods comprising the sample; male, female, or pooled</p>
http://lod.bco-dmo.org/id/dataset-parameter/883636.rdf
Name: Female_inbred_line
Units: unitless
Description: <p>Identifier of inbred line for the females in the sample; VA = SW1 (saline inbred line 1), VE = SW2 (saline inbred line 2) , RA = FW1 (freshwater inbred line 1), RB = FW2 (freshwater inbred line 2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883637.rdf
Name: female_ancestor_location
Units: unitless
Description: <p>Home location of the female ancestor</p>
http://lod.bco-dmo.org/id/dataset-parameter/883638.rdf
Name: Male_inbred_line
Units: unitless
Description: <p>Identifier of inbred line for the males in the sample; VA = SW1 (saline inbred line 1), VE = SW2 (saline inbred line 2) , RA = FW1 (freshwater inbred line 1), RB = FW2 (freshwater inbred line 2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883639.rdf
Name: male_ancestor_location
Units: unitless
Description: <p>Home location of the male ancestor</p>
http://lod.bco-dmo.org/id/dataset-parameter/883640.rdf
Name: Experimental_culture
Units: unitless
Description: <p>Culture identification of inbred lines</p>
http://lod.bco-dmo.org/id/dataset-parameter/883641.rdf
Name: Description
Units: unitless
Description: <p>Experiment description</p>
http://lod.bco-dmo.org/id/dataset-parameter/883642.rdf
Name: Salinity_conditions_rearing
Units: unitless
Description: <p>Salinity conditions in which the copepods were reared</p>
http://lod.bco-dmo.org/id/dataset-parameter/883643.rdf
Name: PSU_culture
Units: PSU
Description: <p>Practical salinity unit value for the culture water (or water in which the copepods were reared)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883644.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/883645.rdf
Name: SRA
Units: unitless
Description: <p>NCBI Sequence Read Archive identifier for sample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/883646.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample number</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
8849
https://darchive.mblwhoilibrary.org/bitstream/1912/29497/1/dataset-883426_gene-expression-eurytemora-affinis-saline-and-freshwater__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.883426.1
download
onLine
dataset
<p><strong>Study objectives</strong><br />
The goal of this study was to explore evolutionary shifts in gene expression between ancestral saline and freshwater invading populations of the <em>Eurytemora affinis</em>&nbsp;(copepod) species complex on a genome-wide scale.&nbsp;</p>
<p>To explore mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, laboratory experiments were conducted using both ancestral saline and derived freshwater populations of <em>Eurytemora affinis</em>.&nbsp;&nbsp;Then&nbsp;<span style="background-color:rgb(255, 255, 255); color:rgb(51, 51, 51); font-family:sans-serif,arial,verdana,trebuchet ms; font-size:13px">RNA-seq data -- Illumina short paired-end (PE) reads (101 base pairs) of 10 freshwater and 12 saline&nbsp;</span><em>E.affinis</em><span style="background-color:rgb(255, 255, 255); color:rgb(51, 51, 51); font-family:sans-serif,arial,verdana,trebuchet ms; font-size:13px">&nbsp;samples --&nbsp;</span>were used to answer the following questions:</p>
<ul>
<li>(1)&nbsp; What are the patterns of evolutionary shifts in gene expression between the ancestral saline and freshwater invading populations?</li>
<li>(2)&nbsp; What are the plastic (acclimatory) changes in gene expression between salinities (0 PSU vs. 15 PSU conditions) within each of the saline and freshwater populations?</li>
<li>(3)&nbsp; Are the magnitude and direction of plasticity in gene expression correlated with evolutionary responses?</li>
<li>(4)&nbsp; Has plasticity in gene expression evolved following freshwater invasions?</li>
</ul>
<p><strong>Collection of ancestral populations</strong><br />
The copepods were collected using a plankton net mesh size&nbsp;of 50 μm&nbsp;in diameter, from a depth of 1-4 meters from near the shore.&nbsp;The freshwater copepods were collected in April-May 2006 by throwing the plankton net off the dock in Racine Harbor, Lake Michigan in Wisconsin, USA (42.729444 N, 87.778889 W). The saline copepods were collected by small boats near the shore in Baie de L'Isle Verte, St. Lawrence marsh, Quebec, Canada (48.003889 N, 69.425278 W)&nbsp;in May-June 2006.&nbsp; Collected samples were transported to the laboratory where&nbsp;<em>Eurytemora affinis</em>&nbsp;individuals were identified and sampled under the microscope.</p>
<p><strong>Laboratory cultures and experiments</strong><br />
Four inbred lines of <em>Eurytemora affinis</em>&nbsp;(two each from the two populations) were generated&nbsp;through full-sibling mating for 30 generations. Two independent saltwater inbred lines (SW1 and SW2) were derived from the ancestral saline population in Baie de L’Isle Verte (Canada) and reared at their native salinity of 15 PSU.&nbsp; The&nbsp;two freshwater inbred lines (FW1 and FW2)&nbsp;were derived from the freshwater invading population in Racine Harbor (USA) and reared in Lake Michigan water (0 PSU, conductivity 300&nbsp;μS/cm). In addition, reciprocal F1 crosses between freshwater and saline inbred lines were created and reared to test for allele-specific expression by comparing gene expression in parental lines and their F1 crosses.</p>
<p>Two replicate common-garden reaction norm experiments, each consisting of a 2 × 2 factorial design, were performed to compare patterns of the gene expression of the FW and SW inbred lines (see Materials and Methods in Posavi et al. 2020).&nbsp; Total RNA from whole bodies of 50 copepods (25 females and 25 males) per sample was extracted using Trizol reagent (Ambion RNA) and Qiagen RNeasy Mini Kit for purification (Qiagen cat. no. 74104). Extracted and purified RNA samples were stored at -80 degrees Celsius until sequencing. The strand-specific Illumina RNA-seq libraries (Parkhomchuk et al., 2009) of polyA purified mRNA were constructed using the TruSeq RNA Sample Prep kit (Illumina). Three biological replicates per inbred line were sequenced using the Illumina HiSeq 2000 platform in the Institute for Genome Sciences at the University of Maryland School of Medicine and generated 101-bp-long paired-end read data.&nbsp;</p>
<p>These data have important implications for understanding&nbsp;the evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats.&nbsp;</p>
<p><strong>Problem report</strong><br />
One replicate of the FW1 inbred line was excluded because of bacterial infection</p>
<p><strong>Additional information</strong><br />
~ Detailed methods, results, and figures can be found in Posavi et al. (2020) (<em>see Related Publications section</em>).&nbsp;<br />
~ The sequence data can be viewed under NCBI BioProject PRJNA278152 (<em>see Related Datasets</em>).</p>
Specified by the Principal Investigator(s)
<p dir="ltr"><span style="background-color:transparent; font-family:arial; font-size:10pt">To assess the taxonomic composition and ensure the provenance of the sample, the RNA-seq reads were screened by the Institute for Genome Sciences' QC pipeline against a local installation of the NCBI nucleotide database. After that, each sample was run through the data processing pipeline to detect the presence of adaptor sequences or low read quality using FastQC (Andrews, 2010). Reads were trimmed with Trimmomatic version 032 (Bolger et al., 2014). On average, 3.5 × 107 paired-end (101 bp) reads per sample passed these filtering steps.</span></p>
<p dir="ltr"><span style="background-color:transparent; font-family:arial; font-size:10pt">To quantify transcript (gene) expression levels, an expectation maximization approach employing the RSEM (RNA-seq by Expectation Maximization) package (Li &amp; Dewey, 2011) was used. The </span><em>Eurytemora affinis </em><span style="background-color:transparent; font-family:arial; font-size:10pt">complex (Atlantic clade, aka </span><em>E. carolleeae</em><span style="background-color:transparent; font-family:arial; font-size:10pt">) draft genome served as the reference genome. Automated gene annotation of this genome was conducted at the Baylor College of Medicine Human Genome Sequencing Center within the i5K pilot project (using Maker2.2 following methods of Holt &amp; Yandell, 2011) </span><span style="font-family:arial; font-size:13.3333px">resulting in 29,783 gene models.&nbsp;&nbsp;</span><span style="background-color:transparent; font-family:arial; font-size:10pt">For additional details on gene annotation, see Eyun et al. (2017).&nbsp; </span></p>
<p dir="ltr"><span style="background-color:transparent; font-family:arial; font-size:10pt">To improve the automated gene annotation, the Cufflinks Tuxedo protocol (Trapnell et al., 2012) was used. The merged gene annotation file was used as input into RSEM to (a) build reference transcript sequences using the prepare-reference and (b) align RNA-seq reads to the reference transcripts and estimate gene and transcript abundances (using rsem-calculate-expression).</span></p>
<p dir="ltr"><span style="background-color:transparent; font-family:arial; font-size:10pt">To map RNA-seq reads to the </span><em>E. affinis </em><span style="background-color:transparent; font-family:arial; font-size:10pt">complex genome, Bowtie2 was employed resulting in 16–30 million mapped paired-end reads. To verify the annotation of DE genes, the manual annotation of the </span><em>E. affinis </em><span style="background-color:transparent; font-family:arial; font-size:10pt">complex genome (using the Web Apollo platform on the i5k Workspace, https://i5k.nal.usda.gov/Eurytemora_affinis) was performed.&nbsp;</span></p>
<p dir="ltr"><span style="background-color:transparent; font-family:arial; font-size:10pt">Structural gene annotation, generated by merging transcriptomes of 22 RNA samples, resulted in 37,827 putative genes. To increase the power to detect differential expression, genes with less than one count-per million (CPM) in at least two samples were filtered out, as were transcripts with best BLASTx matches to bacteria (n = 3), and transcripts without BLASTx hits. These filtering steps left 14,082 putative genes remaining for the differential gene expression analysis, all of which mapped to the </span><em>E. affinis</em><span style="background-color:transparent; font-family:arial; font-size:10pt"> genome assembly. Subsequently, the normalization on 14,082 genes was performed, using the Trimmed Mean of M values method (Robinson &amp; Oshlack, 2010), available in Bioconductor's edgeR package for R software (Chen et al., 2018; Robinson et al., 2009).&nbsp;</span></p>
<p dir="ltr"><span style="background-color:transparent; font-family:arial; font-size:10pt">To identify significant differences in gene expression between saline and freshwater inbred lines (Goal 1) and between salinities (0 and 15 PSU) (Goal 2), statistical analyses using a generalized linear model (GLM) were performed. To detect DE genes, a negative binomial generalized linear model was used that accommodated the complex designs of the common-garden experiments (Bioconductor’s edgeR package with function glmQLFit with option robust= TRUE). To conduct the test for each genotype (inbred line) and salinity combination, the read counts were modeled as the result of the fixed effects of genotype (inbred line effect), salinity (0 and15 PSU), batch, and genotype-by-salinity interactions. For multiple hypothesis testing, we adjusted p-values using the Benjamini and Hochberg (1995) method with a false discovery rate (FDR) threshold of 0.05.&nbsp;</span></p>
<p><strong>Software</strong><br />
(See also&nbsp;Related Publications section below)</p>
<ul>
<li>Bowtie2&nbsp; (Langmead &amp; Salzberg, 2012)</li>
<li>BLASTx&nbsp; (Mukhopadhyay et al., 2017)</li>
<li>Cufflinks Tuxedo protocol (<span style="font-family:arial; font-size:13.3333px">Trapnell et al., 2012)</span></li>
<li>edgeR&nbsp; (Chen et al., 2018; Robinson et al, 2009)</li>
<li>FastQC&nbsp; (Andrews, 2010)</li>
<li>Maker2.2&nbsp; (Holt &amp; Yandell, 2011)</li>
<li>RSEM&nbsp; (Li &amp; Dewey, 2011)</li>
<li>Trimmomatic&nbsp; (<span style="font-family:arial; font-size:13.3333px">Bolger et al., 2014)</span></li>
</ul>
<p><strong>BCO-DMO Processing</strong><br />
- Converted date to Y-M-D format<br />
- Added information about inbred lines for better readability</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 PI Supplied Instrument Description:Libraries were sequenced on an Illumina HiSeq platform at the University of Maryland, School of Medicine, Institute for Genome Sciences. 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.
PI Supplied Instrument Name: Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/