http://lod.bco-dmo.org/id/dataset/1004674
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
2026-08-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pfam differential expression data for diatoms from an iron incubation experiment aboard the R/V Sally Ride during the PUPCYCLE II cruise within the California Current System in May-June 2023
2026-09-13
publication
2026-09-13
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-09-30
publication
https://doi.org/10.26008/1912/bco-dmo.1004674.1
Adrian Marchetti
University of North Carolina at Chapel Hill
principalInvestigator
Natalie Cohen
University of Georgia
principalInvestigator
Astrid Schnetzer
North Carolina State University
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: Speciale, E., Lim, P., Jeong, Y., Cook, C., Cohen, N., McClure, W., Schnetzer, A., Marchetti, A. (2026) Pfam differential expression data for diatoms from an iron incubation experiment aboard the R/V Sally Ride during the PUPCYCLE II cruise within the California Current System in May-June 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-09-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.1004674.1 [access date]
Diatom Pfam differential expression from PUPCYCLE II Dataset Description: <p>This dataset is one of many generated from an iron incubation experiment conducted as part of the PUPCYCLE II cruise in May and June 2023. The different analyses are listed here, with links to other datasets from this study in the Related Datasets section.</p>
<p>Analyses&nbsp;include:</p>
<ul>
<li>Physiology (dataset 994607)
<ul>
<li>Dissolved inorganic nutrients (nitrate, phosphate, silicic acid)</li>
<li>Size-fractionated chlorophyll a</li>
<li>Size-fractionated isotope uptake rates (nitrate and DIC)</li>
<li>Flow cytometry</li>
<li>FlowCAM analysis</li>
<li>FLP experiments for mixotroph cell-specific grazing rates</li>
</ul>
</li>
<li>RNA taxonomy data for normalized reads (dataset 1003525)</li>
<li><strong>Differential expression for +Fe versus DFB treatments at T1 and T2: Pfam</strong>
<ul>
<li>Mixotroph Pfam (dataset 1004659)</li>
<li><strong>Diatom Pfam (this dataset 1004674)</strong></li>
</ul>
</li>
<li>Differential expression for +Fe versus DFB treatments at T1 and T2 for mixotrophs and diatoms: KEGG gene&nbsp;(dataset 1004689)</li>
<li>Differential expression for +Fe versus DFB treatments at T1 and T2 for mixotrophs and diatoms: KEGG pathways (this dataset 1004704)</li>
<li>Dissolved iron concentrations (dataset 1004007)</li>
</ul>
<p>See Related Datasets section below for links to above mentioned datasets.</p> Methods and Sampling: <p>Data collection took place on the R/V Sally Ride from May 29th to June 10th, 2023. To simulate upwelling conditions under different iron treatments, an onboard incubation experiment was conducted. Seawater for the incubation experiment was collected within the northern CCS, off the southern coast of Oregon at 43°02'42.7"N, 124°33'07.2"W. The collected seawater was deemed as freshly upwelled water and taken from a depth of 55 meters – which corresponds to a depth slightly below the euphotic zone receiving less than 1% irradiance – using trace-metal clean techniques on May 30th, 2023, 13:30 GMT. The seawater was pumped and homogenized using trace metal clean techniques, then transferred into a total of thirty 20 L low-density polyethylene cubitainers. Three cubitainers were immediately harvested for the initial timepoint (T0). The remaining twenty-seven cubitainers were assigned treatments: nine were unamended (Ctrl), nine were amended with 5 nM FeCl<sub>2&nbsp;</sub>(+Fe), and nine were amended with 200 nM desferrioxamine B, a strong iron chelator that inhibits dissolved iron uptake (DFB). The cubitainers were placed in an on-deck incubator covered with two layers of neutral density screening to simulate 26% of incident&nbsp;irradiance. The incubator was&nbsp;supplied with flow-through surface seawater to maintain ambient surface temperature. Three cubitainers from each treatment were harvested for each of the three subsequent timepoints: 48 hours (T1), 168 hours (T2), and 264 hours (T3) after incubation.</p>
<p><strong>RNA Collection and Metatranscriptomics.&nbsp;</strong>Cubitainers were harvested for RNA by collecting and filtering approximately 2.5 to 4 L of each sample onto 0.8 μm Pall Supor filters (142 mm) using a peristaltic pump; samples were then immediately flash frozen in liquid nitrogen and stored at -80°C. RNA was extracted using the RNAqueous-4PCR kit, according to the manufacturer's instructions with a few modifications – filters were cut up due to their large size, 200 μL of glass beads were added, and 3 mL of lysis buffer was added. RNA samples were sent to GENEWIZ for library preparation and sequencing with PolyA tail selection. Sequencing was performed on an Illumina HiSeq 4000 with a 2x150 bp configuration. GENEWIZ provided raw paired-end read sequences for each sample.&nbsp;</p>
<p>Raw reads were trimmed using Trim Galore v0.6.10 (Krueger, 2015), which uses Cutadapt (Martin, 2011), and quality control was assessed through FastQC (Andrews, 2010).&nbsp;&nbsp;A&nbsp;<em>de novo&nbsp;</em>metatranscriptome assembly was conducted using rnaSPAdes v3.15.5 for individual assemblies (Bushmanova et al., 2019) and CD-HIT v4.8.1 for a grand assembly (Li &amp; Godzik, 2006). TransDecoder v5.7.1 was used to determine the most likely open reading frame (ORF) for each contig (Haas, 2023). ORFs were annotated using the Marine Functional Eukaryotic Reference Taxa (MarFERReT) database v1.1.1 (e-value &lt; 1e<sup>-06</sup>) (Groussman et al., 2023) for NCBI taxonomies (Federhen, 2011), PR<sup>2</sup>&nbsp;taxonomies (Guillou et al., 2012) and Pfam 34.0 functions (Mistry et al., 2021). To remove any potential bacterial contamination, ORFs were also annotated against the PhyloDB v1076 database using EUKulele (e-value &lt; 1e<sup>-06</sup>) (Krinos et al., 2020). Any ORF with a higher bitscore for a bacteria or virus compared to its MarFERReT annotation was removed (resulting in &lt; 3% of ORFs removed). To maximize functional annotation coverage, ORFs were annotated using eggNOG-mapper v2.1.12 (Cantalapiedra et al., 2021) to obtain annotations from the Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa, 2000). Trimmed samples were then aligned to the grand assembly using Salmon v1.10.3 (Patro et al., 2017) and exported into a comprehensive counts table using tximport (Soneson et al., 2016).&nbsp;Reads not mapping to a protist group as defined by MarFERReT annotations were removed before downstream analysis.&nbsp;</p>
<p>DESeq2 was used to obtain normalized counts and conduct differential expression analyses (Love et al., 2014). Analyses of Pfam protein domains were performed on reads mapping to the lineage Bacillariophyta, hereafter referred to as “diatoms,” as defined by MarFERReT (Groussman et al., 2023). Reads not mapping to the taxonomic group being analyzed were removed before normalization and statistical testing. Reads were then summed by annotation ID (Pfam accession number) before entering the DESeq2 analysis. If a contig was annotated with multiple IDs, its reads were evenly distributed among the mapped annotations.</p>
<p>Differential expression analysis was conducted using the DESeq2 <em>DESeq() </em>function. This workflow estimates size factors using the median-of-ratios method, estimates dispersion, fits a negative binomial generalized linear model, and performs hypothesis testing using the Wald test. P values were adjusted for multiple testing using the Benjamini–Hochberg procedure to control the false discovery rate. Analyses focused on comparisons between +Fe and DFB treatments at T1 and T2. A Pfam protein domain was considered differentially expressed when the absolute value of its log2 fold change (L2FC) was greater than 1 and its adjusted P value (p-adj) was less than 0.05. Normalized counts for each Pfam protein domain were also obtained to determine the relative contributions of each diatom genus to each annotation ID.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1751805 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1751805
completed
Adrian Marchetti
University of North Carolina at Chapel Hill
919-843-3473
123 South Rd.
Chapel Hill
NC
27514
USA
amarchet@email.unc.edu
pointOfContact
Natalie Cohen
University of Georgia
919-519-8297
10 Ocean Science Circle
Savannah
GA
31411
USA
cohen@uga.edu
pointOfContact
Astrid Schnetzer
North Carolina State University
919-515-7837
2800 Faucette Drive 4148 Jordan Hall
Raleigh
NC
27695
USA
aschnet@ncsu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Taxa_Group
Timepoint
DE_Comparison
Pfam_ID
Pfam_Name
Pfam_Description
baseMean
log2FoldChange
lfcSE
stat
pvalue
padj
Amphiprora
Amphora
Asterionellopsis
Astrosyne
Attheya
Aulacoseira
Chaetoceros
Conticribra
Corethron
Coscinodiscus
Craspedostauros
Cyclophora
Cyclotella
Cylindrotheca
Dactyliosolen
Detonula
Ditylum
Entomoneis
Eucampia
Extubocellulus
Fistulifera
Fragilariopsis
Grammatophora
Guinardia
Helicotheca
Leptocylindrus
Licmophora
Mediolabrus
Minidiscus
Minutocellus
Navicula
Naviculales
Nitzschia
Odontella
Phaeodactylum
Pleurosigma
Proboscia
Pseudictyota
Pseudonitzschia
Seminavis
Skeletonema
Stauroneis
Staurosira
Stephanopyxis
Striatella
Synedra
Synedropsis
Thalassionema
Thalassiosira
Thalassiothrix
Trieres
Tryblionella
Latitude
Longitude
Illumina HiSeq 4000
Niskin bottle
theme
None, User defined
taxon
time_point
treatment
accession number
Pfam database domain name
mean
fold change
standard error
Wald z-statistic
p-value
normalized sequence read count
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Niskin bottle
instrument
BCO-DMO Standard Instruments
SR2311
service
Deployment Activity
California Current System
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.
CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans
https://osprey.bco-dmo.org/project/768006
CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans
<p><em>NSF Award Abstract:</em><br />
Upwelling zones are hotspots of photosynthesis that are very dynamic in space and time. Microscopic algae, known as phytoplankton, bloom when deep, nutrient-rich waters are upwelled into sunlit surface layers of the ocean, providing nourishment that supports productive food webs and draws down carbon dioxide (CO2) from the atmosphere to the deep ocean. Photosynthetic microbes in these regions must constantly adapt to changes in their chemical and physical environments. For example, subsurface populations respond to changes in light as they approach the surface. When upwelled waters move offshore, cells sink out of the illuminated zone, establishing seed populations that remain inactive until the next upwelling event. This process is called the upwelling conveyor belt cycle (UCBC). How phytoplankton respond to these changes in environmental conditions and how they may influence their nutrient requirements remains unknown. With future ocean changes predicted to alter seawater chemistry, including ocean acidification and decreased iron availability, some phytoplankton groups may be more vulnerable than others. Accompanying educational activities provide learning experiences to enhance understanding and awareness of marine microbes. The development of a research hub at UNC aims to provide infrastructure and support for scientists and students conducting research on environmental genomics. A laboratory component for an upper-level undergraduate course focused on marine phytoplankton is being developed. Educational outreach activities to broader communities include creation of a lesson plan on phytoplankton in upwelling zones and a virtual research cruise experience for middle-school students, as well as a hands-on lab activity for a local museum focused on marine phytoplankton and the important roles they play in shaping our planet.</p>
<p>The project examines how phytoplankton respond at the molecular and physiological level to the different UCBC stages, which seed populations (i.e., surface versus subsurface) contribute most to phytoplankton blooms during upwelling events of varying intensity, how phytoplankton elemental compositions are altered throughout UCBC stages, and how future predicted ocean conditions will affect the phytoplankton responses to UCBC conditions. This project contains both laboratory and fieldwork. In the laboratory, phytoplankton isolates recently obtained from upwelling regions are exposed to simulated UCBC conditions to examine changes in gene expression, growth and photosynthetic characteristics and elemental composition. Cultures are subjected to both current and future ocean conditions, including reduced iron availability and higher CO2. In the field, research cruises within upwelling regions study the dynamics of natural phytoplankton communities (both surface and subsurface) experiencing upwelling and relaxation and within simulated upwelling incubation experiments. Knowledge of how phytoplankton are affected by UCBC conditions at an integrated molecular, physiological and elemental level under both current and future scenarios is imperative for the proper conservation and management of these critically important ecosystems.</p>
Upwelled Phytoplankton Dynamics
largerWorkCitation
project
eng; USA
biota
oceans
California Current System
-124.552
-124.552
43.045194
43.045194
2023-05-29
2023-06-10
California Upwelling Zone
0
BCO-DMO catalogue of parameters from Pfam differential expression data for diatoms from an iron incubation experiment aboard the R/V Sally Ride during the PUPCYCLE II cruise within the California Current System in May-June 2023
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/1007697.rdf
Name: Taxa_Group
Units: unitless
Description: <p>Taxa group being targeted for differential expression analysis. All reads not mapping to the targeted taxa group were removed prior to analysis.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007698.rdf
Name: Timepoint
Units: unitless
Description: <p>Timepoint identification (T1 or T2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007699.rdf
Name: DE_Comparison
Units: unitless
Description: <p>Treatments being targeted for differential expression analysis. This will always be +FevsDFB, representing the iron-replete (+Fe) vs iron-limited (DFB) treatments.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007700.rdf
Name: Pfam_ID
Units: unitless
Description: <p>Number ID of Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007701.rdf
Name: Pfam_Name
Units: unitless
Description: <p>Short name of Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007702.rdf
Name: Pfam_Description
Units: unitless
Description: <p>Long name of Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007703.rdf
Name: baseMean
Units: number of normalized reads
Description: <p>The average expression level of the Pfam domain across all samples (normalized).</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007704.rdf
Name: log2FoldChange
Units: unitless
Description: <p>DESeq2-estimated log2 fold change in Pfam-domain expression for +Fe (iron-amended treatment) relative to DFB (iron-limited treatment); positive values indicate higher expression in +Fe and negative values indicate higher expression in DFB</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007705.rdf
Name: lfcSE
Units: unitless
Description: <p>Standard error of log2FoldChange estimate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007706.rdf
Name: stat
Units: unitless
Description: <p>Test statistic used in Wald test to determine significance; log2FoldChange divided by lfcSE, which is used to generate a two-tailed p-value via the Wald Test</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007707.rdf
Name: pvalue
Units: unitless
Description: <p>Raw p-value from Wald test.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007708.rdf
Name: padj
Units: unitless
Description: <p>The False Discovery Rate adjusted p-value using the Benjamini-Hochberg correction.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007709.rdf
Name: Amphiprora
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Amphiprora contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007710.rdf
Name: Amphora
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Amphora contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007711.rdf
Name: Asterionellopsis
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Asterionellopsis contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007712.rdf
Name: Astrosyne
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Astrosyne contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007713.rdf
Name: Attheya
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Attheya contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007714.rdf
Name: Aulacoseira
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Aulacoseira contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007715.rdf
Name: Chaetoceros
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Chaetoceros contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007716.rdf
Name: Conticribra
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Conticribra contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007717.rdf
Name: Corethron
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Corethron contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007718.rdf
Name: Coscinodiscus
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Coscinodiscus contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007719.rdf
Name: Craspedostauros
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Craspedostauros contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007720.rdf
Name: Cyclophora
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Cyclophora contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007721.rdf
Name: Cyclotella
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Cyclotella contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007722.rdf
Name: Cylindrotheca
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Cylindrotheca contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007723.rdf
Name: Dactyliosolen
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Dactyliosolen contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007724.rdf
Name: Detonula
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Detonula contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007725.rdf
Name: Ditylum
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Ditylum contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007726.rdf
Name: Entomoneis
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Entomoneis contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007727.rdf
Name: Eucampia
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Eucampia contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007728.rdf
Name: Extubocellulus
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Extubocellulus contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007729.rdf
Name: Fistulifera
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Fistulifera contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007730.rdf
Name: Fragilariopsis
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Fragilariopsis contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007731.rdf
Name: Grammatophora
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Grammatophora contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007732.rdf
Name: Guinardia
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Guinardia contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007733.rdf
Name: Helicotheca
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Helicotheca contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007734.rdf
Name: Leptocylindrus
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Leptocylindrus contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007735.rdf
Name: Licmophora
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Licmophora contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007736.rdf
Name: Mediolabrus
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Mediolabrus contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007737.rdf
Name: Minidiscus
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Minidiscus contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007738.rdf
Name: Minutocellus
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Minutocellus contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007739.rdf
Name: Navicula
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Navicula contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007740.rdf
Name: Naviculales
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom order Naviculales contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007741.rdf
Name: Nitzschia
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Nitzschia contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007742.rdf
Name: Odontella
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Odontella contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007743.rdf
Name: Phaeodactylum
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Phaeodactylum contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007744.rdf
Name: Pleurosigma
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Pleurosigma contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007745.rdf
Name: Proboscia
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Proboscia contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007746.rdf
Name: Pseudictyota
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Pseudictyota contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007747.rdf
Name: Pseudonitzschia
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Pseudo-nitzschia contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007748.rdf
Name: Seminavis
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Seminavis contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007749.rdf
Name: Skeletonema
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Skeletonema contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007750.rdf
Name: Stauroneis
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Stauroneis contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007751.rdf
Name: Staurosira
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Staurosira contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007752.rdf
Name: Stephanopyxis
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Stephanopyxis contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007753.rdf
Name: Striatella
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Striatella contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007754.rdf
Name: Synedra
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Synedra contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007755.rdf
Name: Synedropsis
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Synedropsis contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007756.rdf
Name: Thalassionema
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Thalassionema contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007757.rdf
Name: Thalassiosira
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Thalassiosira contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007758.rdf
Name: Thalassiothrix
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Thalassiothrix contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007759.rdf
Name: Trieres
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Trieres contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007760.rdf
Name: Tryblionella
Units: number of normalized reads
Description: <p>The number of normalized reads that the diatom genera Tryblionella contributes to the Pfam domain.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007761.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sampling station</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007763.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sampling station</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
https://doi.org/10.26008/1912/bco-dmo.1004674.1
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dataset
<p>Data collection took place on the R/V Sally Ride from May 29th to June 10th, 2023. To simulate upwelling conditions under different iron treatments, an onboard incubation experiment was conducted. Seawater for the incubation experiment was collected within the northern CCS, off the southern coast of Oregon at 43°02'42.7"N, 124°33'07.2"W. The collected seawater was deemed as freshly upwelled water and taken from a depth of 55 meters – which corresponds to a depth slightly below the euphotic zone receiving less than 1% irradiance – using trace-metal clean techniques on May 30th, 2023, 13:30 GMT. The seawater was pumped and homogenized using trace metal clean techniques, then transferred into a total of thirty 20 L low-density polyethylene cubitainers. Three cubitainers were immediately harvested for the initial timepoint (T0). The remaining twenty-seven cubitainers were assigned treatments: nine were unamended (Ctrl), nine were amended with 5 nM FeCl<sub>2&nbsp;</sub>(+Fe), and nine were amended with 200 nM desferrioxamine B, a strong iron chelator that inhibits dissolved iron uptake (DFB). The cubitainers were placed in an on-deck incubator covered with two layers of neutral density screening to simulate 26% of incident&nbsp;irradiance. The incubator was&nbsp;supplied with flow-through surface seawater to maintain ambient surface temperature. Three cubitainers from each treatment were harvested for each of the three subsequent timepoints: 48 hours (T1), 168 hours (T2), and 264 hours (T3) after incubation.</p>
<p><strong>RNA Collection and Metatranscriptomics.&nbsp;</strong>Cubitainers were harvested for RNA by collecting and filtering approximately 2.5 to 4 L of each sample onto 0.8 μm Pall Supor filters (142 mm) using a peristaltic pump; samples were then immediately flash frozen in liquid nitrogen and stored at -80°C. RNA was extracted using the RNAqueous-4PCR kit, according to the manufacturer's instructions with a few modifications – filters were cut up due to their large size, 200 μL of glass beads were added, and 3 mL of lysis buffer was added. RNA samples were sent to GENEWIZ for library preparation and sequencing with PolyA tail selection. Sequencing was performed on an Illumina HiSeq 4000 with a 2x150 bp configuration. GENEWIZ provided raw paired-end read sequences for each sample.&nbsp;</p>
<p>Raw reads were trimmed using Trim Galore v0.6.10 (Krueger, 2015), which uses Cutadapt (Martin, 2011), and quality control was assessed through FastQC (Andrews, 2010).&nbsp;&nbsp;A&nbsp;<em>de novo&nbsp;</em>metatranscriptome assembly was conducted using rnaSPAdes v3.15.5 for individual assemblies (Bushmanova et al., 2019) and CD-HIT v4.8.1 for a grand assembly (Li &amp; Godzik, 2006). TransDecoder v5.7.1 was used to determine the most likely open reading frame (ORF) for each contig (Haas, 2023). ORFs were annotated using the Marine Functional Eukaryotic Reference Taxa (MarFERReT) database v1.1.1 (e-value &lt; 1e<sup>-06</sup>) (Groussman et al., 2023) for NCBI taxonomies (Federhen, 2011), PR<sup>2</sup>&nbsp;taxonomies (Guillou et al., 2012) and Pfam 34.0 functions (Mistry et al., 2021). To remove any potential bacterial contamination, ORFs were also annotated against the PhyloDB v1076 database using EUKulele (e-value &lt; 1e<sup>-06</sup>) (Krinos et al., 2020). Any ORF with a higher bitscore for a bacteria or virus compared to its MarFERReT annotation was removed (resulting in &lt; 3% of ORFs removed). To maximize functional annotation coverage, ORFs were annotated using eggNOG-mapper v2.1.12 (Cantalapiedra et al., 2021) to obtain annotations from the Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa, 2000). Trimmed samples were then aligned to the grand assembly using Salmon v1.10.3 (Patro et al., 2017) and exported into a comprehensive counts table using tximport (Soneson et al., 2016).&nbsp;Reads not mapping to a protist group as defined by MarFERReT annotations were removed before downstream analysis.&nbsp;</p>
<p>DESeq2 was used to obtain normalized counts and conduct differential expression analyses (Love et al., 2014). Analyses of Pfam protein domains were performed on reads mapping to the lineage Bacillariophyta, hereafter referred to as “diatoms,” as defined by MarFERReT (Groussman et al., 2023). Reads not mapping to the taxonomic group being analyzed were removed before normalization and statistical testing. Reads were then summed by annotation ID (Pfam accession number) before entering the DESeq2 analysis. If a contig was annotated with multiple IDs, its reads were evenly distributed among the mapped annotations.</p>
<p>Differential expression analysis was conducted using the DESeq2 <em>DESeq() </em>function. This workflow estimates size factors using the median-of-ratios method, estimates dispersion, fits a negative binomial generalized linear model, and performs hypothesis testing using the Wald test. P values were adjusted for multiple testing using the Benjamini–Hochberg procedure to control the false discovery rate. Analyses focused on comparisons between +Fe and DFB treatments at T1 and T2. A Pfam protein domain was considered differentially expressed when the absolute value of its log2 fold change (L2FC) was greater than 1 and its adjusted P value (p-adj) was less than 0.05. Normalized counts for each Pfam protein domain were also obtained to determine the relative contributions of each diatom genus to each annotation ID.</p>
Specified by the Principal Investigator(s)
<p dir="ltr">Differential expression analyses for Pfam protein domains were performed for reads mapping to the lineage Bacillariophyta as defined by MarFERReT (henceforth referred to as diatoms). Reads not mapping to the taxa group being analyzed were removed prior to normalization and statistical testing. Reads were summed based on annotation ID (Pfam accession number) prior to entering DESeq2 analysis; if a contig annotated to multiple IDs, its reads were evenly distributed between the mapped annotations. A protein domain was considered differentially expressed if the absolute value of log2FoldChange (L2FC) &gt; 1 and the p-adjusted value (p-adj) &lt; 0.05</p>
<p>The metatranscriptomic pipeline code used for this project is publicly available at https://github.com/emilyspeciale/Speciale-Metatranscriptomics.&nbsp;</p>
<p><strong>Software:</strong>&nbsp;Trim Galore v0.6.10; FastQC&nbsp;v0.12.1; rnaSPAdes v3.15.5; CD-HIT v4.8.1; TransDecoder v5.7.1; EUKulele v2.0.9; eggNOG-mapper v2.1.12; Salmon v1.10.3; &nbsp;tximport v1.3.9; DESeq2 v1.42.1.</p>
<p><strong>Databases/reference resources:</strong>&nbsp;MarFERReT v1.1.1; NCBI Taxonomy; PR2; Pfam 34.0; PhyloDB v1076;&nbsp;<span style="font-family:arial,sans-serif; font-size:13.3333px">Kyoto Encyclopedia of Genes and Genomes (KEGG)</span>; Mixoplankton Database (MDB).</p>
<ul>
<li>1. Raw reads were trimmed with Trim Galore v0.6.10 (Krueger, 2015)</li>
<li>2. Read quality was assessed with FastQC v0.12.1 (Andrews, 2010)</li>
<li>3.&nbsp;<em>De novo</em> metatranscriptome assemblies were generated&nbsp;using rnaSPAdes v3.15.5 (Bushmanova et al., 2019) for individual assemblies and&nbsp;CD-HIT v4.8.1 (Li &amp; Godzik, 2006) for the grand assembly</li>
<li>4. ORFs were identified with&nbsp;TransDecoder v5.7.1 (Haas, 2023).&nbsp;</li>
<li>5. Taxonomy and functional annotation via Marine&nbsp;Functional Eukaryotic Reference Taxa (MarFERReT) database v1.1.1 (Groussman et al., 2023); includes&nbsp;NCBI taxonomies (Federhen, 2011),&nbsp;PR2 taxonomies (Guillou et al., 2012), and&nbsp;Pfam 34.0 functions (Mistry et al., 2021).&nbsp;</li>
<li>6. PhyloDB v1076 filtering using EUKulele v2.0.9 (Krinos et al., 2020).&nbsp;</li>
<li>7. eggNOG-mapper v2.1.12 (Cantalapiedra et al., 2021) /&nbsp;KEGG annotation (Kanehisa, 2000)</li>
<li>8. Reads were quantified with Salmon v1.10.3 (Patro et al., 2017)&nbsp;</li>
<li>9. Reads were imported with tximport v1.3.9 (Soneson et al., 2016)</li>
<li>10. Taxonomic filtering where reads outside the target taxonomic group were removed</li>
<li>11. Annotation-ID read summation</li>
<li>12. DESeq2 v1.42.1 (Love et al., 2014) was used to compare +Fe versus DFB at T1 and T2</li>
</ul>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
CURATION ACTIONS PERFORMED ON DATA
- Loaded source file "BCO_DMO_PUPCYCLEII_DiaPfamDE.csv" into the BCO-DMO system converting missing data identifier NA to empty cell
- Added latitude and longitude of sampling station
- Set data types to string for first 6 columns, and all other columns formatted as numeric
- Columns with p-value and padj were set to scientific notation to match how they appeared in the original file
- Reordered diatom genera to be in alphabetical order
- Exported final file as "1004674_v1_diatom_pfam.csv"
CURATION ACTIONS PERFORMED ON METADATA
- Changed in-line citations to have format of (author, year) replacing numbered references.
- Corrected first sentence of Abstract to say diatoms rather than mixotrophs
- Corrected minor typos and punctuation
ISSUES POTENTIALLY IMPACTING REUSE
- N/A
Specified by BCO-DMO Data Managers
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 4000
Illumina HiSeq 4000
PI Supplied Instrument Name: Illumina HiSeq 4000 PI Supplied Instrument Description:Sequencing was performed on an Illumina HiSeq 4000 with a 2x150 bp configuration. 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.
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Niskin bottles were used to collect the seawater used for metatranscriptomics Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: SR2311
SR2311
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
SR2311
Adrian Marchetti
University of North Carolina at Chapel Hill
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel