Dataset: Flow Cytometry Results

Name: Results of the quantification of symbiont cell numbers from 400 Acropora hyacinthus colonies subjected to experimental bleaching in the summer of 2018 in Palau.
Published: 2020-06-23
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.813210.1

Spatial Extent: N:7.92908 E:134.66061 S:7.20388 W:134.21919

Temporal Extent: 2018-07 - 2018-08

Project:

Predicting the global location of heat tolerant corals: Palau patch reefs as a general model (Heat Tolerant Corals)

Lead Principal Investigator:

Stephen R. Palumbi (Stanford University)

BCO-DMO Data Manager:

Christina Haskins (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-06-23

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Results of the quantification of symbiont cell numbers from 400 Acropora hyacinthus colonies subjected to experimental bleaching in the summer of 2018 in Palau.

Abstract:

Results of the quantification of symbiont cell numbers from 400 Acropora hyacinthus colonies subjected to experimental bleaching in the summer of 2018 in Palau.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-06-23	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.813210.1	2020-07-08

Methods & Sampling

These samples were collected according to the protocol published by Krediet et al. 2015: Article Rapid, Precise, and Accurate Counts of Symbiodinium Cells Using the Guava Flow Cytometer, and a Comparison to Other Methods

The samples that were analyzed for this study are 400 colonies of Acropora hyacinthus. Nubbins from each colony were experimentally bleached at temperatures of 34, 34.5 and 35 degrees Celsius as well as two control treatments (30 deg. C). These nubbins were then airbrushed and the resulting tissue slurry was preserved in RNAlater. Tissue dissociation and preparation for analysis on the Guava EasyCyte flow cytometer followed the protocol by Krediet et al. 2015.

Procedures followed Krediet et al. 2015 (above), with the exception that protein concentration was not measured.

Data Processing Description

All data were processed with the software accompanying the Guava easyCyte flow cytometer.

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* Renamed column headers and set types
* rounded decimal numbers to precision of 2
* blank values in this dataset are displayed as "nd" for "no data." nd is the default missing data identifier in the BCO-DMO system.

Data Files

File
flowcyt.csv (Comma Separated Values (.csv), 450.49 KB) MD5:a682b435b2b69a8a8103be1f515b0edc Primary data file for dataset ID 813210

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1736736

Deployments

None available yet

Instruments

Flow Cytometer

Supplied Name: Guava easyCyte HT 2-laser flow cytometer (Millipore)

Supplied Description:

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample	Colony Number	dimensionless	sample
Treatment	Treatment (C1 and C2 are control), all others are heat stress	unitless	treatment
Temperature	Specific Temperature treatment	degrees Celsius	temperature
Sample_ID	Unique sample ID (technical replicates have the same SampleID)	dimensionless	sample
ALLEVENTS_Conc	Concentration (cells/ml) of events above gating threshold	cells/ml	cell_concentration
SYMBIODINIUM_Conc	Concentration (cells/ml) of events above gating threshold that are also above the symbiodinium gating threshold	cells/ml	cell_concentration
Number_of_Events	Number of events counted (max 5000)	unitless	count
Cell_Count	Concentration (cells/ul) of events above gating threshold	cells/ul	cell_concentration
Total_Volume	Total volume of sample measured in microliters	microliters	volume
Acquisition_Time	Total acquisition time on instrument in seconds	seconds	time_elapsed
Negative_Total_Count	Number of events above gating threshold in negative control	various	cell_concentration
Negative_Events	Concentration of cells (cells/ml) in negative control above gating threshold	cells/ml	cell_concentration
Negative_Sym_Conc	Concentration of symbiont cells in negative control above gating threshold	various	cell_concentration
Negative_Cells	Concentration of cells (cells/ul) in negative control above gating threshold	cell/ul	cell_concentration
Negative_Total_Vol	Total volume of negative control measured in microliters	microliters	volume
Negative_Acquisition_Time	Total acquisistion time on instrument for negative control in seconds	seconds	time_elapsed