BCO-DMO ERDDAP
Accessing BCO-DMO data 		log in    
Brought to you by BCO-DMO    
 
 
Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Uni-algal, non-axenic cultures of Heterosigma akashiwo (CCMP2393) were grown\nin L1 medium (without silicate) made with a Long Island Sound seawater base\ncollected from Avery Point, CT, USA (salinity 32) at 18\\u00b0C with a 14:10\n(light:dark) cycle with an irradiance of approximately 100 \\u00b5mol m-2 s-1 .\nCells were acclimated in exponential growth phase to different carbonate\nchemistries in 1.2 L of L1 media in 2.5-L polycarbonate bottles. To control\nthe carbonate chemistry of the water, the headspace of each bottle was purged\ncontinuously with a custom gas mixture of ~21% oxygen, ~79% nitrogen and\neither 200, 400, 600, 800 or 1000 ppmv CO2 (TechAir, NY).\n \nAt the point of harvest, 150 mL (~6 x 106 cells) were filtered on to 5 \\u00b5m\npore size, 25 mm polycarbonate filter and flash frozen in liquid nitrogen.\nGenetic material from samples was extracted with the RNeasy Mini kit (Qiagen,\nValencia, CA) and DNA was removed on-column using the RNase-free DNase Set\n(Qiagen), yielding total RNA. Total RNA extracts of the triplicate cultures\nwere quantified on a 2100 Bioanalyzer (Agilent, Santa Clara, CA). Libraries\nwere prepared using poly-A pull down with the TruSeq Stranded mRNA Library\nPrep kit (Illumina, San Diego, CA). Library preparation, barcoding, and\nsequencing from each library was performed by the JP Sulzberger Columbia\nUniversity Genome Center (New York, NY).\n \nSequence reads were de-multiplexed and trimmed to remove sequencing barcodes.\nReads were aligned using Bowtie2 (Langmead and Salzberg 2012) to the MMETSP\nconsensus contigs for Heterosigma akashiwo CCMP2393 ([https://omictools.com\n/marine-microbial-eukaryotic-transcriptome-\nsequenci...](\\\\\"https://omictools.com/marine-microbial-eukaryotic-\ntranscriptome-sequencing-project-tool\\\\\")).\n \nSignificant differences between physiological parameters by CO2 treatment were\nassessed with analysis of variance (ANOVA) and Tukey\\u2019s honestly\nsignificant differences test (aov and TukeyHSD, stats, R). Differential\nexpression of genes in any CO2 treatment compared to modern was determined\nusing the general linear model (GLM) exact test (edgeR, R). Briefly, the read\ncounts were normalized by trimmed mean of M-values (TMM) using the function\ncalcNormFactors, tagwise dispersions were calculated with the function\nestimateGLMTagwiseDisp, a GLM was fit using glmFit, and log2 fold change\n(logFC) for each treatment was calculated relative to average expression at\nmodern CO2. P-values from likelihood ratio tests were corrected for multiple\ntesting using the false discovery method (fdr).
attribute NC_GLOBAL awards_0_award_nid String 55197
attribute NC_GLOBAL awards_0_award_number String OCE-1314336
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1314336 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Hak_acclim \n   The harmful alga Heterosigma akashiwo (CCMP2393) grown under a range of CO2 concentrations from 200-1000 ppm. \n   PI's: S. Dyhrman (LDEO), J. Morris (U Alabama) \n   version: 2018-10-11 \n    See also: https://www.ncbi.nlm.nih.gov/bioproject/377729
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2018-10-11T18:15:14Z
attribute NC_GLOBAL date_modified String 2019-03-18T18:41:47Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.747872.1
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/747872 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to prepare the mRNA libraries. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 747879
attribute NC_GLOBAL instruments_0_description String General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_0_supplied_name String Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit (Illumina, San Diego, CA)
attribute NC_GLOBAL keywords String accession, alkalinity, bco, bco-dmo, biological, biomaterial, biomaterial_provider, biome, bioproject, bioproject_accession, carbon, carbon dioxide, chemical, chemistry, co2, CO2_ppm, collected, collected_by, collection, dark, data, dataset, date, depth, dioxide, dmo, earth, Earth Science > Oceans > Ocean Chemistry > pH, env, env_biome, erddap, genotype, geo, geo_loc_name, history, host, isolate, isolation, isolation_source, latitude, level, light, light_dark_hr, light_level_umol_m2_s, loc, management, media, name, ocean, oceanography, oceans, office, organism, passage, passage_history, ppm, preliminary, provider, reported, samp, samp_size, sample, sample_name, sample_title, sample_type, scale, science, sea, sea_water_ph_reported_on_total_scale, seawater, size, source, strain, temp_C, temperature, time, title, total, type, umol, water
attribute NC_GLOBAL keywords_vocabulary String GCMD Science Keywords
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/747872/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/747872 (external link)
attribute NC_GLOBAL param_mapping String {'747872': {'collection_date': 'flag - time', 'depth': 'master - depth'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/747872/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Lamont-Doherty Earth Observatory
attribute NC_GLOBAL people_0_affiliation_acronym String LDEO
attribute NC_GLOBAL people_0_person_name String Sonya T. Dyhrman
attribute NC_GLOBAL people_0_person_nid String 51101
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String University of Alabama at Birmingham
attribute NC_GLOBAL people_1_affiliation_acronym String UA/Birmingham
attribute NC_GLOBAL people_1_person_name String James Jeffrey Morris
attribute NC_GLOBAL people_1_person_nid String 51678
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Lamont-Doherty Earth Observatory
attribute NC_GLOBAL people_2_affiliation_acronym String LDEO
attribute NC_GLOBAL people_2_person_name String Gwenn Hennon
attribute NC_GLOBAL people_2_person_nid String 546456
attribute NC_GLOBAL people_2_role String Scientist
attribute NC_GLOBAL people_2_role_type String originator
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Nancy Copley
attribute NC_GLOBAL people_3_person_nid String 50396
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String P-ExpEv
attribute NC_GLOBAL projects_0_acronym String P-ExpEv
attribute NC_GLOBAL projects_0_description String Note: This project is also affiliated with the NSF BEACON Center for the Study of Evolution in Action.\nProject Description from NSF Award:\nHuman activities are driving up atmospheric carbon dioxide  concentrations at an unprecedented rate, perturbing the ocean's  carbonate buffering system, lowering oceanic pH, and changing the  concentration and composition of dissolved inorganic carbon. Recent  studies have shown that this ocean acidification has many short-term  effects on phytoplankton, including changes in carbon fixation among  others. These physiological changes could have profound effects on  phytoplankton metabolism and community structure, with concomitant  effects on Earth's carbon cycle and, hence, global climate. However,  extrapolation of present understanding to the field are complicated by  the possibility that natural populations might evolve in response to  their changing environments, leading to different outcomes than those  predicted from short-term studies. Indeed, evolution experiments  demonstrate that microbes are often able to rapidly adapt to changes in  the environment, and that beneficial mutations are capable of sweeping  large populations on time scales relevant to predictions of  environmental dynamics in the coming decades. This project addresses two  major areas of uncertainty for phytoplankton populations with the  following questions:\n1) What adaptive mutations to elevated CO2 are  easily accessible to extant species, how often do they arise, and how  large are their effects on fitness?\n2) How will physical and ecological  interactions affect the expansion of those mutations into standing  populations?\nThis study will address these questions by coupling  experimental evolution with computational modeling of ocean  biogeochemical cycles. First, cultured unicellular phytoplankton,  representative of major functional groups (e.g. cyanobacteria, diatoms,  coccolithophores), will be evolved under simulated year 2100 CO2  concentrations. From these experiments, estimates will be made of a) the  rate of beneficial mutations, b) the magnitude of fitness gains  conferred by these mutations, and c) secondary phenotypes (i.e.,  trade-offs) associated with these mutations, assayed using both  physiological and genetic approaches. Second, an existing numerical  model of the global ocean system will be modified to a) simulate the  effects of changing atmospheric CO2 concentrations on ocean chemistry,  and b) allow the introduction of CO2-specific adaptive mutants into the  extant populations of virtual phytoplankton. The model will be used to  explore the ecological and biogeochemical impacts of beneficial  mutations in realistic environmental situations (e.g. resource  availability, predation, etc.). Initially, the model will be applied to  idealized sensitivity studies; then, as experimental results become  available, the implications of the specific beneficial mutations  observed in our experiments will be explored.\nThis interdisciplinary study will provide novel, transformative  understanding of the extent to which evolutionary processes influence  phytoplankton diversity, physiological ecology, and carbon cycling in  the near-future ocean. One of many important outcomes will be the  development and testing of nearly-neutral genetic markers useful for  competition studies in major phytoplankton functional groups, which has  applications well beyond the current proposal.
attribute NC_GLOBAL projects_0_end_date String 2017-05
attribute NC_GLOBAL projects_0_geolocation String Experiment housed in laboratories at Michigan State University
attribute NC_GLOBAL projects_0_name String Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2
attribute NC_GLOBAL projects_0_project_nid String 2276
attribute NC_GLOBAL projects_0_start_date String 2013-06
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String bioproject_accession,organism,strain,isolate,host,isolation_source,geo_loc_name,sample_type,biomaterial_provider,collected_by,depth,env_biome,genotype,passage_history,samp_size,temp_C,light_level_umol_m2_s,light_dark_hr
attribute NC_GLOBAL summary String This dataset includes metadata associated with NCBI BioProject PRJNA377729 \\Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2\\ PRJNA377729: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729. The alga Heterosigma akashiwo was grown at CO2 levels from about 200 to 1000 ppm and then the DNA and RNA were sequenced.
attribute NC_GLOBAL time_coverage_end String 2017-07-13
attribute NC_GLOBAL time_coverage_start String 2017-06-21
attribute NC_GLOBAL title String [Heterosigma akashiwo acclimation] - NCBI accessions of the harmful alga Heterosigma akashiwo (CCMP2393) grown under a range of CO2 concentrations from 200-1000 ppm (Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable sample_name String
attribute sample_name bcodmo_name String sample
attribute sample_name description String A unique name for the sample
attribute sample_name long_name String Sample Name
attribute sample_name nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample_name units String unitless
variable sample_title String
attribute sample_title bcodmo_name String sample
attribute sample_title description String Title of the sample
attribute sample_title long_name String Sample Title
attribute sample_title nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample_title units String unitless
variable bioproject_accession String
attribute bioproject_accession bcodmo_name String accession number
attribute bioproject_accession description String The accession number of the BioProject(s) to which the BioSample belongs.
attribute bioproject_accession long_name String Bioproject Accession
attribute bioproject_accession units String unitless
variable organism String
attribute organism bcodmo_name String taxon
attribute organism description String The most descriptive organism name for this sample
attribute organism long_name String Organism
attribute organism units String unitless
variable strain String
attribute strain bcodmo_name String unknown
attribute strain description String The microbial or eukaryotic strain name
attribute strain long_name String Strain
attribute strain units String unitless
variable isolate double
attribute isolate _FillValue double NaN
attribute isolate bcodmo_name String unknown
attribute isolate description String Identification or description of the specific individual from which this sample was obtained
attribute isolate long_name String Isolate
attribute isolate units String unitless
variable host double
attribute host _FillValue double NaN
attribute host bcodmo_name String unknown
attribute host description String The natural (as opposed to laboratory) host to the organism from which the sample was obtained.
attribute host long_name String Host
attribute host units String unitless
variable isolation_source double
attribute isolation_source _FillValue double NaN
attribute isolation_source bcodmo_name String site
attribute isolation_source description String Describes the physical - environmental and/or local geographical source of the biological sample from which the sample was derived.
attribute isolation_source long_name String Isolation Source
attribute isolation_source units String unitless
variable time double
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.4980032E9, 1.499904E9
attribute time axis String T
attribute time bcodmo_name String date
attribute time description String Date of sampling formatted as yyyy-mm-dd
attribute time ioos_category String Time
attribute time long_name String Collection Date
attribute time nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute time source_name String collection_date
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time time_precision String 1970-01-01
attribute time units String seconds since 1970-01-01T00:00:00Z
variable geo_loc_name String
attribute geo_loc_name bcodmo_name String site
attribute geo_loc_name description String Geographical origin of the sample
attribute geo_loc_name long_name String Geo Loc Name
attribute geo_loc_name units String unitless
variable sample_type String
attribute sample_type bcodmo_name String sample_descrip
attribute sample_type description String Sample type
attribute sample_type long_name String Sample Type
attribute sample_type units String unitless
variable biomaterial_provider String
attribute biomaterial_provider bcodmo_name String laboratory
attribute biomaterial_provider description String Name and address of the lab or PI or a culture collection identifier
attribute biomaterial_provider long_name String Biomaterial Provider
attribute biomaterial_provider units String unitless
variable collected_by double
attribute collected_by _FillValue double NaN
attribute collected_by bcodmo_name String person
attribute collected_by description String Name of persons or institute who collected the sample
attribute collected_by long_name String Collected By
attribute collected_by units String unitless
variable depth double
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth colorBarMaximum double 8000.0
attribute depth colorBarMinimum double -8000.0
attribute depth colorBarPalette String TopographyDepth
attribute depth description String Sample collection depth
attribute depth ioos_category String Location
attribute depth long_name String Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable env_biome String
attribute env_biome bcodmo_name String site_descrip
attribute env_biome description String Descriptor of the broad ecological context of a sample.
attribute env_biome long_name String Env Biome
attribute env_biome units String unitless
variable genotype double
attribute genotype _FillValue double NaN
attribute genotype bcodmo_name String sample_descrip
attribute genotype description String Observed genotype
attribute genotype long_name String Genotype
attribute genotype units String unitless
variable lat_lon double
attribute lat_lon _FillValue double NaN
attribute lat_lon bcodmo_name String latitude
attribute lat_lon colorBarMaximum double 90.0
attribute lat_lon colorBarMinimum double -90.0
attribute lat_lon description String latitude and longitude of sample colllection
attribute lat_lon long_name String Latitude
attribute lat_lon nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute lat_lon source_name String lat_lon
attribute lat_lon standard_name String latitude
attribute lat_lon units String decimal degrees
variable passage_history String
attribute passage_history bcodmo_name String treatment
attribute passage_history description String Number of passages and passage method
attribute passage_history long_name String Passage History
attribute passage_history units String unitless
variable samp_size String
attribute samp_size bcodmo_name String cell_concentration
attribute samp_size description String Amount or size of sample that was collected
attribute samp_size long_name String Samp Size
attribute samp_size units String unitless
variable temp_C byte
attribute temp_C _FillValue byte 127
attribute temp_C actual_range byte 18, 18
attribute temp_C bcodmo_name String temperature
attribute temp_C description String Temperature of the sample at time of sampling
attribute temp_C long_name String Temp C
attribute temp_C nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute temp_C units String degrees Celsius
variable light_level_umol_m2_s byte
attribute light_level_umol_m2_s _FillValue byte 127
attribute light_level_umol_m2_s actual_range byte 100, 100
attribute light_level_umol_m2_s bcodmo_name String irradiance
attribute light_level_umol_m2_s description String Light level
attribute light_level_umol_m2_s long_name String Light Level Umol M2 S
attribute light_level_umol_m2_s nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/VSRW/ (external link)
attribute light_level_umol_m2_s units String micromol photons m-2 s-1
variable light_dark_hr String
attribute light_dark_hr bcodmo_name String duration
attribute light_dark_hr description String duration of light and dark cycles
attribute light_dark_hr long_name String Light Dark Hr
attribute light_dark_hr units String hours
variable Media String
attribute Media bcodmo_name String unknown
attribute Media description String Type of growth medium used
attribute Media long_name String Media
attribute Media units String unitless
variable CO2_ppm float
attribute CO2_ppm _FillValue float NaN
attribute CO2_ppm actual_range float 206.64, 1051.43
attribute CO2_ppm bcodmo_name String pCO2
attribute CO2_ppm description String CO2 concentration
attribute CO2_ppm long_name String CO2 Ppm
attribute CO2_ppm nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/ (external link)
attribute CO2_ppm units String parts per million
variable Alkalinity short
attribute Alkalinity _FillValue short 32767
attribute Alkalinity actual_range short 2029, 2096
attribute Alkalinity bcodmo_name String TALK
attribute Alkalinity description String Alkalinity of sample
attribute Alkalinity long_name String Alkalinity
attribute Alkalinity nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/ (external link)
attribute Alkalinity units String micromol per kilogram (umol/kg)
variable pH float
attribute pH _FillValue float NaN
attribute pH actual_range float 7.54, 8.14
attribute pH bcodmo_name String pH
attribute pH colorBarMaximum double 9.0
attribute pH colorBarMinimum double 7.0
attribute pH description String The measure of the acidity or basicity of an aqueous solution
attribute pH long_name String Sea Water Ph Reported On Total Scale
attribute pH nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/ (external link)
attribute pH units String unitless; pH scale

 
ERDDAP, Version 2.22
Disclaimers | Privacy Policy | Contact