Metadata Report for BODC Series Reference Number 2008034
Metadata Summary
Problem Reports
Data Access Policy
Narrative Documents
Project Information
Data Activity or Cruise Information
Fixed Station Information
BODC Quality Flags
SeaDataNet Quality Flags
Metadata Summary
Data Description |
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Data Identifiers |
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Time Co-ordinates(UT) |
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Spatial Co-ordinates | |||||||||||||||||||||||||||||||||||||
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Parameters |
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Problem Reports
No Problem Report Found in the Database
Data Access Policy
Open Data supplied by Natural Environment Research Council (NERC)
You must always use the following attribution statement to acknowledge the source of the information: "Contains data supplied by Natural Environment Research Council."
Narrative Documents
BD Biosciences Influx Cell Sorter
The BD Influx cell sorter is a flow cytometry platform with modular architecture and a combination of detection capabilities and hands-on controls. The optical system has up to ten lasers that can be customized with detectors and filters. The BD Influx system can handle a throughput rate of up to 200,000 events per second and features two, four and six way sorting as well as plate sorting. A unique fluidics system protects cells and addresses contamination. The nozzle assembly is designed to produce high droplet frequencies at relatively low pressures, enabling high-speed sorting while maintaining cell viability and functionality. To simplify drop-delay determination the BD FACS Accudrop technology is used. The BD Influx supports up to six-way sorting to maximize efficiency, and plate sorting to accommodate isolation of single cells. The Influx uses BD FACS Software sorter software. To prevent cross-contamination the complete fluidics system from sheath tank to nozzle top can be exchanged.
The core of the BD Influx system is the nozzle assembly which features an optimized acoustical coupling, enabling efficient droplet formation. This design minimizes noise from the droplet formation process and results in high droplet formation rates at relatively low sheath pressures. A sample station and fluidics console controls sample flow, sample line backflush, boost and differential pressure. The form of the nozzle enables cells to accelerate smoothly to the laser intercept, with a variety of nozzle sizes available. Bubble detectors prevent air bubbles from reaching the nozzle by stopping flow when the sample tube is empty.
The 10 laser paths and 7-pinhole optical collection system support 24 parameters simultaneously and 24 x 24 compensation. Systems with up to 5 lasers support 16 simultaneous parameters and 16 x 16 compensation. For each laser, light is shaped by individual optics and final alignment and focusing are achieved using a dedicated lens.
Specifications
| Specification | Description |
|---|---|
| Drop Drive Frequency | Adjustable 9-180 kHz |
| Nozzles | Supplied: 70, 86, 100, and 140 µm Optional: 200 µm |
| Data Acquisition Channels | Up to 5-laser systems: 16 channels, usually 14 colors plus forward and side scatter. Systems with 6 lasers or more: 24 channels, usually 22 colors plus forward and side scatter |
| Signal Processing | 16-bit analog-to-digital conversion, 65,536 channels |
| Acquisition Rate | Dead time is 0 ms. The maximum throughput rate is 200,000 events per second, independent of the number of parameters. |
| Fluorescence Compensation | Up to 5-laser systems: 16 x 16 digital compensation matrix. Systems with 6 lasers or more: 24 x 24 digital compensation matrix. |
| Fluidics Reservoirs | Autoclavable 7-L sheath and waste containers, equipped with pressure and vacuum readout, are provided. |
| Sample Input | 12 x 75-mm tubes, polypropylene |
| Fluidics General Operation | Sheath pressure is adjustable from 1-90 psi (0.07-6.2 bar). |
| Bubble Detector | A bubble detector in the sample line detects air bubbles from the sample tube and stops sample flow when the sample tube is empty, preventing air bubbles from reaching the nozzle assembly. |
| Temperature Control | Sample input and sort collection tubes can be cooled or heated by an optional circulating water bath. |
Non-toxic (underway) sea water supply
A source of uncontaminated near-surface (commonly 3 to 7 m) seawater pumped continuously to shipboard laboratories on research vessels. There is typically a temperature sensor near the intake (known as the hull temperature) to provide measurements that are as close as possible to the ambient water temperature. The flow from the supply is typically directed through continuously logged sensors such as a thermosalinograph and a fluorometer. Water samples are often collected from the non-toxic supply. The system is also referred to as the underway supply.
Phytoplankton Abundance by Automated Flow Cytometry (AFC) analysis of surface underway samples collected during AMT22 (JC079)
Originator's Protocol for Data Acquisition and Analysis
Discrete samples were collected from the ship's underway seawater supply. For each of these underway samples the following parameters were determined:
- Phytoplankton carbon biomass
- Flow-cytometric analysis (Graff et al. 2012)
- Particle size distribution
- Particulate organic carbon
- Phytoplankton pigments (High Performance Liquid Chromatography)
Live phytoplankton cells were identified and counted immediately using a BD Biosciences Influx flow cytometer (model 104S). The Flow cytometer was equipped with the Forward Scatter Small Particle Option. Particles were excited with a blue (488 nm) laser and used Chlorophyll (692 nm) fluorescence as the trigger parameter. Synechococcus were identified by high phycoerythryn fluorescence (530 nm). Other taxa were based on chlorophyll (692 nm) fluorescence and scatter. Phytoplankton concentrations were calculated using a time-volume calibration and the time it took to record each file.
References Cited
Graff, J.R., Milligan, A.J., Behrenfeld, M.J. . 2012. The measurement of phytoplankton biomass using flow-cytometric sorting and elemental analysis of carbon. Limnol. Oceanogr.: Methods.
Instrumentation Description
BD Biosciences Influx flow cytometer (model 104S)
BODC Data Processing Procedures
Data were submitted via email in an Excel spreadsheet archived under BODC's accession number OPP140092. Sample metadata (Sample ID, latitude, longitude, Date, Time (GMT) and year day) were checked against information held in the database.
The data were provided in cell abundance per millilitre. These units were consistent with the BODC parameter code units so no conversions were necessary.
The data were reformatted and marked up with BODC parameter codes. Data were loaded to into BODC's samples database under Oracle Relational Database Management System using established BODC data banking procedures.
A parameter mapping table is provided below;
| Originator's Parameter | Units | Description | BODC Parameter Code | Units | Comments |
|---|---|---|---|---|---|
| Synechococcus spp. | cell abundance ml-1 | Abundance of Synechococcus spp. (ITIS: 773: WoRMS 160572) per unit volume of the water body by automated flow cytometry | P700A90Z | cell abundance ml-1 | n/a |
| Prochlorococcus spp. | cell abundance ml-1 | Abundance of Prochlorococcus spp. (ITIS: 610076: WoRMS 345515) per unit volume of the water body by automated flow cytometry | P701A90Z | cell abundance ml-1 | n/a |
| Pico-eukaryotes | cell abundance ml-1 | Abundance of Picoeukaryotic cells per unit volume of the water body by automated flow cytometry | PYEUA00A | cell abundance ml-1 | n/a |
| Nanoeukaryotes | cell abundance ml-1 | Abundance of nanoeukaryotic cells [Size: 2-12 µm] per unit volume of the water body by automated flow cytometry | X726A86B | cell abundance ml-1 | n/a |
Data Quality Report
BODC were not advised of specific quality checks carried out by the data originators. There were no stand out values in the sample data provided to BODC.
Problem Report
Not relevant to this data set.
Project Information
Oceans 2025 Theme 10, Sustained Observation Activity 1: The Atlantic Meridional Transect (AMT)
The Atlantic Meridional Transect has been operational since 1995 and through the Oceans 2025 programme secures funding for a further five cruises during the period 2007-2012. The AMT programme began in 1995 utilising the passage of the RRS James Clark Ross between the UK and the Falkland Islands southwards in September and northwards in April each year. Prior to Oceans 2025 the AMT programme has completed 18 cruises following this transect in the Atlantic Ocean. This sustained observing system aims to provide basin-scale understanding of the distribution of planktonic communities, their nutrient turnover and biogenic export in the context of hydrographic and biogeochemical provinces of the North and South Atlantic Oceans.
The Atlantic Meridional Transect Programme is an open ocean in situ observing system that will:
- give early warning of any fundamental change in Atlantic ecosystem functionng
- improve forecasts of the future ocean state and associated socio-economic impacts
- provide a "contextual" logistical and scientific infrastructure for independently-funded national and international open ocean biogeochemical and ecological research.
The specific objectives are:
- To collect hydrographic, chemical, ecological and optical data on transects between the UK and the Falkland Islands
- To quantify the nature and causes of ecological and biogeochemical variability in planktonic ecosystems
- To assess the effects of variability in planktonic ecosystems on biogenic export and on air-sea exchange of radiatively active gases
The measurements taken and experiments carried out on the AMT cruises will be closely linked to Themes 2 and 5. The planned cruise track also allows for the AMT data to be used in providing spatial context to the Sustained Observation Activities at the Porcupine Abyssal Plain Ocean Observatory (SO2) and the Western Channel Observatory (SO10).
More detailed information on this Work Package is available at pages 6 - 9 of the official Oceans 2025 Theme 10 document: Oceans 2025 Theme 10
Weblink: http://www.oceans2025.org/
Data Activity or Cruise Information
Cruise
| Cruise Name | JC079 (AMT22) |
| Departure Date | 2012-10-10 |
| Arrival Date | 2012-11-24 |
| Principal Scientist(s) | Glen A Tarran (Plymouth Marine Laboratory) |
| Ship | RRS James Cook |
Complete Cruise Metadata Report is available here
Fixed Station Information
No Fixed Station Information held for the Series
BODC Quality Control Flags
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
| Flag | Description |
|---|---|
| Blank | Unqualified |
| < | Below detection limit |
| > | In excess of quoted value |
| A | Taxonomic flag for affinis (aff.) |
| B | Beginning of CTD Down/Up Cast |
| C | Taxonomic flag for confer (cf.) |
| D | Thermometric depth |
| E | End of CTD Down/Up Cast |
| G | Non-taxonomic biological characteristic uncertainty |
| H | Extrapolated value |
| I | Taxonomic flag for single species (sp.) |
| K | Improbable value - unknown quality control source |
| L | Improbable value - originator's quality control |
| M | Improbable value - BODC quality control |
| N | Null value |
| O | Improbable value - user quality control |
| P | Trace/calm |
| Q | Indeterminate |
| R | Replacement value |
| S | Estimated value |
| T | Interpolated value |
| U | Uncalibrated |
| W | Control value |
| X | Excessive difference |
SeaDataNet Quality Control Flags
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
| Flag | Description |
|---|---|
| 0 | no quality control |
| 1 | good value |
| 2 | probably good value |
| 3 | probably bad value |
| 4 | bad value |
| 5 | changed value |
| 6 | value below detection |
| 7 | value in excess |
| 8 | interpolated value |
| 9 | missing value |
| A | value phenomenon uncertain |
| B | nominal value |
| Q | value below limit of quantification |
