http://lod.bco-dmo.org/id/dataset/739636
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
2018-07-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification.
2025-02-27
publication
2025-02-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-11-20
publication
https://doi.org/10.1575/1912/bco-dmo.739636.1
Christopher Dupont
J. Craig Venter Institute
principalInvestigator
Alyson E. Santoro
University of California-Santa Barbara
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: Dupont, C., Santoro, A. (2018) Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-07-10 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.739636.1 [access date]
Thaumarchaea transcriptomes Dataset Description: <p>Nitrosopelagicus brevis CN25 and U25 were grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing.</p> Methods and Sampling: <p>Thaumarchaea transcriptomes sequences.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1259994 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1259994
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260006 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260006
completed
Christopher Dupont
J. Craig Venter Institute
858-200-1886
9704 Medical Center Drive
Rockville
MD
20850
USA
cdupont@jcvi.org
pointOfContact
Alyson E. Santoro
University of California-Santa Barbara
805-893-5318
2155 Marine Biotech Lab
Santa Barbara
CA
93106
USA
asantoro@ucsb.edu
pointOfContact
asNeeded
Dataset Version: 1.1
Unknown
Accession_url
Accession_text
Accession
Sample_Name
Organism
Tax_ID
Strain
Illumina NextSEQ 500
theme
None, User defined
external_link
accession number
sample identification
species scientific name (binomial)
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.
Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea
https://osprey.bco-dmo.org/project/555307
Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea
<p><em>NSF award abstract:</em></p>
<p>Intellectual Merit. How organisms respond to their physical and chemical and environment is a central question in marine ecology. For microbes living in the mesopelagic - the ocean's "twilight zone" - an efficient response is particularly important to capitalize on the intermittent delivery of organic and inorganic compounds sinking from the surface ocean. These organisms must have a suite of metabolic and regulatory strategies used to cope with environmental variability, but these strategies are largely unknown. Understanding when and why metabolic genes are expressed is critical to our understanding of nutrient remineralization in the ocean. Marine group 1 (MG1) archaea are ubiquitous, abundant microbes in the meso- and bathypelagic and promising model organisms for investigating these questions. MG1 archaea are chemolithoautotrophs that oxidize ammonia for energy and fix carbon for biomass, and as such, play a central role in the ocean's coupled carbon and nitrogen cycles. Though MG1 have historically eluded cultivation, recent efforts have been successful at bringing representative MG1 archaea from the open ocean into culture and demonstrating their importance in the production of the greenhouse gas nitrous oxide. This project takes advantage of unique MG1 cultures and the recently sequenced draft genome of one of the organisms - strain CN25 - to investigate the physiological and transcriptional responses of MG1 archaea to variations in their chemical environment, specifically:</p>
<p>1. Comparative transcriptomics of CN25 cells grown under a range of energy availability and nitrosative stress will identify select genes that can be used to diagnose the physiological state of natural populations</p>
<p>2. Improvements in the genomic and transcriptomic knowledge of MG1 archaea will facilitate a thorough reinterpretation of existing metagenomic and metatranscriptomic datasets, as well as provide a better contextual understanding in future studies</p>
<p>The investigators will conduct comparative transcriptomics of CN25 cells harvested in mid-exponential growth and stationary phase versus starved cells. Transcriptomes of cells grown at high nitrate concentrations and low pO2 with those grown in standard conditions will be characterized. A strand-specific, high-density RNAseq approach will be used to examine the expression of putative ORFs, polycistronic operons, and small RNAs, which, in addition to gene expression profiling, has the ancillary benefit of improving genome annotation. Finally, the investigators will sequence the genomes of two additional MG1 strains isolated from the open ocean, as well as single cells from environmental surveys, and leverage the combination with the CN25 genome to reanalyze available metagenomic and metatranscriptomic datasets. The results will define the transcriptional response of a model mesopelagic microbe to a range of chemical environments, and show how the physicochemical environment induces changes in gene expression and gene content that result in greenhouse gas production. This work will rapidly generate new knowledge of how some of the most ubiquitous, yet heretofore elusive, microorganisms respond to geochemical variability and shape our evolving understanding of the marine nitrogen cycle.</p>
<p>Broader Impacts. The scientific and societal impact of the project will be to elucidate the mechanisms of greenhouse gas production in a model marine organism that is of broad interest to biological and chemical oceanographers. Transcriptome sequencing will improve the assembly of the CN25 genome, the first genome of an MG1 archaeon from the open ocean. Both the genome and transcriptomes will be important references for researchers using metagenomics, metatranscriptomics, and metaproteomics in the ocean, as these techniques are reliant on a knowledgebase composed of both DNA sequence and physiology. Thus, the results add value to both existing and future studies. The proposed research will advance education, teaching, and training for the next generation of marine scientists by providing support for two early-career investigators, one postdoctoral researcher, and a secondary school teacher.</p>
AmoA Archaea
largerWorkCitation
project
eng; USA
oceans
-76.070137
-76.070137
38.57506
38.57506
2025-02-27
Epipelagic and mesopelagic, Equatorial Pacific
0
BCO-DMO catalogue of parameters from Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification.
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/954934.rdf
Name: Accession_url
Units: unitless
Description: <p>Link to NCBI Accession link</p>
http://lod.bco-dmo.org/id/dataset-parameter/954935.rdf
Name: Accession_text
Units: unitless
Description: <p>NCBI Accession Number</p>
http://lod.bco-dmo.org/id/dataset-parameter/739741.rdf
Name: Accession
Units: unitless
Description: <p>Accession number and NCBI link</p>
http://lod.bco-dmo.org/id/dataset-parameter/739742.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/739743.rdf
Name: Organism
Units: unitless
Description: <p>Species of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/739744.rdf
Name: Tax_ID
Units: unitless
Description: <p>Taxonomic identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/739745.rdf
Name: Strain
Units: unitless
Description: <p>Strain identification</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
2823
https://darchive.mblwhoilibrary.org/bitstream/1912/24865/1/dataset-739636_thaumarchaea-transcriptomes__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.739636.1
download
onLine
dataset
<p>Thaumarchaea transcriptomes sequences.</p>
Specified by the Principal Investigator(s)
<p>Libraries were sequenced in one 300 cycle NextSEQ run. Raw Illumina reads in fastq format are interleaved to match paired ends. Sequencing primers and barcode indexes were identified by BLAST against the NCBI vector database and trimmed along with regions with Q scores &lt; 30. Reads mapping to ribosomal RNAs were identified and removed using ribopicker.</p>
<p>Reads were mapped (clc_ref_assemble_long –s 0.9, CLC genomics) to the Ca. N. brevis strains CN25 or U25 genome sequences. Raw read counts per open reading frame (ORF) were compiled.</p>
<p><strong>BCO-DMO Data Processing Notes:</strong></p>
<p>- Included links to NCBI via accession numbers<br />
- Reformatted column names to comply with BCO-DMO standards</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 NextSEQ 500
Illumina NextSEQ 500
PI Supplied Instrument Name: Illumina NextSEQ 500 PI Supplied Instrument Description:Used to identify samples 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.