http://lod.bco-dmo.org/id/dataset/773272
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
2019-07-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accession numbers and related metadata from a study of transcriptomic response of Emiliania huxleyi to 2-heptyl-4-quinolone (HHQ)
2019-07-16
publication
2019-07-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-07-31
publication
https://doi.org/10.26008/1912/bco-dmo.773272.1
Kristen E. Whalen
Haverford College
principalInvestigator
Elizabeth Harvey
Skidaway Institute of Oceanography
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: Whalen, K., Harvey, E. (2020) NCBI accession numbers and related metadata from a study of transcriptomic response of Emiliania huxleyi to 2-heptyl-4-quinolone (HHQ). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-07-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.773272.1 [access date]
Transcriptomic response of Emiliania huxleyi to HHQ Dataset Description: <p>Sequences from this study are available at the NCBI GEO under accession series GSE131846 <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&amp;acc=GSE131846" target="_blank">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&amp;acc=GSE131846</a></p> Methods and Sampling: <p>Batch 2 L cultures of axenic Emiliania huxleyi strain CCMP2090 were grown in natural seawater-based f/2-Si medium (Guillard 1975) in sterile acid-washed polycarbonate bottles. Cultures were maintained on a 14:10 light (80 +/- 5 µmol photons m⁻² s⁻¹):dark cycle at 17.5 - 17.8 ᵒC. After 48 hr of growth, quadruplicate 2 L cultures were exposed to either 1 ng/ml, 10 ng/ml, or 100 ng/ml concentrations of 2-heptyl-4-quinolone (HHQ). Quadruplicate bottles were also exposed to dimethyl sulfoxide (DMSO) to serve as a vehicle control (final concentration 0.002% DMSO in all bottles). Cell biomass was collected 24 hr and 72 hr after treatment via centrifugation (9,000 RPM for 8 min at 4 ᵒC) of 400 ml of culture and total RNA extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommendations using 350 µl RLT plus buffer per sample and the optional centrifugation (14,000 RPM for 1 min) step to ensure membranes were dry prior to elution with 30 µl RNase free water. Eluent was reapplied to the membrane, and incubated for 8 min at room temperature before repeating the elution step to increase yield. Strand-specific RNAseq library construction was performed using the KAPA Stranded mRNA-Seq library preparation kit with KAPA mRNA capture beads (Kapa Biosystems) and sequenced on the NextSeq platform (Illumina) to generate 75 bp paired-end reads.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657808 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657808
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657818 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657818
completed
Kristen E. Whalen
Haverford College
610-795-6042
370 Lancaster Ave. KINSC S314
Haverford
PA
19041
USA
kwhalen1@haverford.edu
pointOfContact
Elizabeth Harvey
Skidaway Institute of Oceanography
NH
USA
elizabeth.harvey@unh.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
series_accession
biosample_accession
biosample_link
sample_name
organism
tax_ID
strain
sample_type
biomaterial_provider
env_biome
samp_size
temp
light_level_umol_m2_s
light_dark_hr
media
collection_date
geo_loc_name
treatment
time_elapsed
bio_replicate
llumina NextSeq500
theme
None, User defined
accession number
sample description
species scientific name (binomial)
laboratory
site description
cell_concentration
water temperature at measurement depth
irradiance
duration
treatment
date
site
time_elapsed
replicate
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
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.
Collaborative Research: Building a framework for the role of bacterial-derived chemical signals in mediating phytoplankton population dynamics
https://osprey.bco-dmo.org/project/709948
Collaborative Research: Building a framework for the role of bacterial-derived chemical signals in mediating phytoplankton population dynamics
<p><em>NSF Award Abstract:</em><br />
Bacteria and phytoplankton play a central role in the modification and flow of materials and nutrients through the marine environment. While it has been established that interactions between these two domains are complex, the mechanisms that underpin these interactions remain largely unknown. There is increasing recognition, however, that dissolved chemical cues govern these microbial interactions. This project focuses on establishing a mechanistic framework for how bacterially derived signaling molecules influence interactions between phytoplankton and bacteria. The quorum-sensing (QS) molecule, 2-heptyl-4-quinolone (HHQ) will be used as a model compound for these investigations. Previously published work suggests that exposure to very low levels of HHQ results in phytoplankton mortality. Gaining a mechanistic understanding of these ecologically important interactions will help to inform mathematical models for the accurate prediction of the cycling of material through the marine microbial loop. This work initiates a new, hybrid workshop-internship undergraduate research program in chemical ecology, with a focus</p>
<p>Bacteria and phytoplankton play a central role in the modification and flow of materials and nutrients through the marine environment. While it has been established that interactions between these two domains are complex, the mechanisms that underpin these interactions remain largely unknown. There is increasing recognition, however, that dissolved chemical cues govern these microbial interactions. This project focuses on establishing a mechanistic framework for how bacterially derived signaling molecules influence interactions between phytoplankton and bacteria. The quorum-sensing (QS) molecule, 2-heptyl-4-quinolone (HHQ) will be used as a model compound for these investigations. Previously published work suggests that exposure to very low levels of HHQ results in phytoplankton mortality. Gaining a mechanistic understanding of these ecologically important interactions will help to inform mathematical models for the accurate prediction of the cycling of material through the marine microbial loop. This work initiates a new, hybrid workshop-internship undergraduate research program in chemical ecology, with a focus into bacteria-phytoplankton interactions. Undergraduate students participate in an intense summer learning experience where research and field-based exercises are supplemented with short-lecture based modules. Students return to their home institutions and work closely with the PIs to conduct interdisciplinary research relating to the aims and scope of the summer research. This research also provides training and career development to two graduate students and a postdoctoral scientist.</p>
<p>Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and microbial trophic structure in the ocean. The intricate relationships between these two domains of life are mediated via excreted molecules that facilitate communication and determine competitive outcomes. Despite their predicted importance, identifying these released compounds has remained a challenge. The PIs recently identified a bacterial QS molecule, HHQ, produced by globally distributed marine gamma-proteobacteria, which induces phytoplankton mortality. The PIs therefore hypothesize that bacteria QS signals are critical drivers of phytoplankton population dynamics and, ultimately, biogeochemical fluxes. This project investigates the timing and magnitude of HHQ production, and the physiological and transcriptomic responses of susceptible phytoplankton species to HHQ exposure, and quantifies the influence of HHQ on natural algal and bacterial assemblages. The work connects laboratory and field-based experiments to understand the governance of chemical signaling on marine microbial interactions, and has the potential to yield broadly applicable insights into how microbial interactions influence biogeochemical fluxes in the marine environment.</p>
HHQSignals
largerWorkCitation
project
eng; USA
oceans
2018-06-20
2018-06-23
Bergen, Norway
0
BCO-DMO catalogue of parameters from NCBI accession numbers and related metadata from a study of transcriptomic response of Emiliania huxleyi to 2-heptyl-4-quinolone (HHQ)
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/773349.rdf
Name: series_accession
Units: unitless
Description: <p>NCBI GEO identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/773350.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/773351.rdf
Name: biosample_link
Units: unitless
Description: <p>URL for SRA BioSample Page at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/773352.rdf
Name: sample_name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/773353.rdf
Name: organism
Units: unitless
Description: <p>NCBI taxonomy name</p>
http://lod.bco-dmo.org/id/dataset-parameter/773354.rdf
Name: tax_ID
Units: unitless
Description: <p>NCBI taxonomy ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/773355.rdf
Name: strain
Units: unitless
Description: <p>Organism strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/773356.rdf
Name: sample_type
Units: unitless
Description: <p>Sample type</p>
http://lod.bco-dmo.org/id/dataset-parameter/773357.rdf
Name: biomaterial_provider
Units: unitless
Description: <p>Name of the lab or PI or a culture collection identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/773358.rdf
Name: env_biome
Units: unitless
Description: <p>Descriptor of the broad ecological contxt of a sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/773359.rdf
Name: samp_size
Units: unitless
Description: <p>Amount of size of sample that was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/773360.rdf
Name: temp
Units: degrees Celsius
Description: <p>Temperature of the sample at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/773361.rdf
Name: light_level_umol_m2_s
Units: microml photons m-2 s-1
Description: <p>Light level</p>
http://lod.bco-dmo.org/id/dataset-parameter/773362.rdf
Name: light_dark_hr
Units: hours
Description: <p>Duration of light and dark cycles</p>
http://lod.bco-dmo.org/id/dataset-parameter/773363.rdf
Name: media
Units: unitless
Description: <p>Type of growth medium used</p>
http://lod.bco-dmo.org/id/dataset-parameter/773364.rdf
Name: collection_date
Units: unitless
Description: <p>Date sample was collected; format: DD-Mmm-YYYY</p>
http://lod.bco-dmo.org/id/dataset-parameter/773365.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geographical origin of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/773366.rdf
Name: treatment
Units: unitless
Description: <p>Treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/773367.rdf
Name: time_elapsed
Units: hours
Description: <p>Time elapsed since treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/773368.rdf
Name: bio_replicate
Units: unitless
Description: <p>Biological replicate 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
16117
https://darchive.mblwhoilibrary.org/bitstream/1912/26036/1/dataset-773272_transcriptomic-response-emiliania-huxleyi-hhq__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.773272.1
download
onLine
dataset
<p>Batch 2 L cultures of axenic Emiliania huxleyi strain CCMP2090 were grown in natural seawater-based f/2-Si medium (Guillard 1975) in sterile acid-washed polycarbonate bottles. Cultures were maintained on a 14:10 light (80 +/- 5 µmol photons m⁻² s⁻¹):dark cycle at 17.5 - 17.8 ᵒC. After 48 hr of growth, quadruplicate 2 L cultures were exposed to either 1 ng/ml, 10 ng/ml, or 100 ng/ml concentrations of 2-heptyl-4-quinolone (HHQ). Quadruplicate bottles were also exposed to dimethyl sulfoxide (DMSO) to serve as a vehicle control (final concentration 0.002% DMSO in all bottles). Cell biomass was collected 24 hr and 72 hr after treatment via centrifugation (9,000 RPM for 8 min at 4 ᵒC) of 400 ml of culture and total RNA extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommendations using 350 µl RLT plus buffer per sample and the optional centrifugation (14,000 RPM for 1 min) step to ensure membranes were dry prior to elution with 30 µl RNase free water. Eluent was reapplied to the membrane, and incubated for 8 min at room temperature before repeating the elution step to increase yield. Strand-specific RNAseq library construction was performed using the KAPA Stranded mRNA-Seq library preparation kit with KAPA mRNA capture beads (Kapa Biosystems) and sequenced on the NextSeq platform (Illumina) to generate 75 bp paired-end reads.</p>
Specified by the Principal Investigator(s)
<p>Sequenced reads were conservatively trimmed to remove adaptors, low-complexity and low-quality sequence, and rRNA reads (including chloroplast and mitochondria rRNA) using Trimmomatic (V0.38; Bolger et al. 2014) with a custom adapter file containing Emiliania huxleyi CCMP2090 rRNA sequences and the following settings: ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 MAXINFO:40:0.5 MINLEN:50. Read quality was examined before and after trimming using FastQC (V0.11.8; <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_blank">https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a>) and MultiQC (V1.6; Ewels et al. 2016). Paired files produced by Trimmomatic were then concatenated prior to determination of transcript abundances using Salmon (V0.12.0; Patro et al. 2017) and the Ensembl (Kersey et al. 2017) gene predictions for Emiliania huxleyi CCMP1516 (the non-axenic form of CCMP2090; <a href="ftp://ftp.ensemblgenomes.org/pub/protists/release-41/fasta/emiliania_huxleyi/cdna/" target="_blank">ftp://ftp.ensemblgenomes.org/pub/protists/release-41/fasta/emiliania_huxleyi/cdna/</a>) as a transcript target index (k-mer size = 23). Salmon was run in the quasi-mapping mode with default settings and the following flags: --validateMappings and –gcBias. Quantification results from Salmon were examined using MultiQC (V1.6; Ewels et al. 2016) and then processed using the tximport R package with default settings (V1.10.0; Soneson et al. 2015) to prepare for gene-level analyses. Transcript and gene IDs were linked using the general feature format file for Emiliania huxleyi CCMP1516 available from Ensembl Genomes (<a href="ftp://ftp.ensemblgenomes.org/pub/protists/release-41/gff3/emiliania_huxleyi" target="_blank">ftp://ftp.ensemblgenomes.org/pub/protists/release-41/gff3/emiliania_huxleyi</a>). Normalization and determination of significantly differentially abundant transcripts was preformed using the DESeq2 R package (V1.22.1; Love et al. 2014) using standard functions and workflows recommended by the authors. After estimation of size factors to normalize for differences in library sequencing depth and gene dispersion estimation using the biological replicates, tests for differential expression were carried out for each pairwise comparison of interest with the Wald test using a negative binomial generalized linear model. Logarithmic fold change (LFC) estimates were shrunken by calling the apeglm package (V1.6.0; Zhu et al. 2018) within DESeq2. The resulting p values were adjusted for multiple testing using the Benjamini-Hochberg (BH) procedure and transcripts with a BH-adjusted p value &lt; 0.1 were deemed to be differentially abundant.</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
llumina NextSeq500
llumina NextSeq500
PI Supplied Instrument Name: llumina NextSeq500 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.