Dataset: RNA:DNA measurements - field data

Name: RNA:DNA measurements for field-collected animals from the Gulf of Mexico Estuary near Port Aransas and Mud Island, Texas from 2020 to 2021
Published: 2023-09-12
Keywords: oceans

Cite This Dataset

Spatial Extent: N:27.9362 E:-97.0218 S:27.8396 W:-97.0827

Temporal Extent: 2020-07-04 - 2021-09-21

Project:

Counter-gradient Flow of Fatty Acids in Marine Food Webs Through Egg Boons (Egg Boon Food Webs)

Principal Investigator:

Lee A. Fuiman (University of Texas - Marine Science Institute, UTMSI)

Co-Principal Investigator:

Parvathi Nair (University of Texas - Marine Science Institute, UTMSI)

Contact:

Lee A. Fuiman (University of Texas - Marine Science Institute, UTMSI)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-09-12

Restricted:

Release Date:

2024-08-01

Validated:

Yes

Current State:

Final no updates expected

RNA:DNA measurements for field-collected animals from the Gulf of Mexico Estuary near Port Aransas and Mud Island, Texas from 2020 to 2021

Abstract:

RNA:DNA measurements for field-collected animals from the Gulf of Mexico Estuary near Port Aransas and Mud Island, Texas from 2020 to 2021.

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Methods & Sampling

Location: Gulf of Mexico Estuary near Port Aransas, Texas. FAML: pier at in Corpus Christi Channel, Port Aransas, TX, United States, Fisheries and Mariculture Laboratory of the University of Texas Marine Science Institute (lat. 27.8396111, lon. -97.0827222); MI: Mud Island in Aransas Bay, TX, United States (lat. 27.9362222, lon. -97.0217777)).

RNA:DNA ratios, which are indicators of animal condition, were measured for samples of egg consumers collected from the field as well as those used in laboratory experiments. Samples of small fishes were collected with cast nets or seines. Fishes were euthanized with lethal dose of MS-222. The euthanized fish were placed on ice and muscle plugs were collected. All samples were lyophilized and stored at -80°C until being processed for RNA:DNA analysis. The time between collection and analysis ranged from 15 to 444 days. Results of the analysis were reported as the ratio of RNA content to DNA content.

Measurements of RNA:DNA were made on individuals. DNA and RNA were measured using the ethidium bromide (EB) fluorometric technique (Westerman and Holt 1988) based on aliquots (10 µL) of homogenates. Calculations were based upon comparisons with DNA-EB and RNA-EB calibration curves from calf thymus DNA and yeast RNA (Type 111) standards. RNA:DNA ratios were normalized using a standardization factor based on the common RNA:DNA slope ratio procedure described by Caldarone et al. (2006). Results of the analysis were reported as the ratio of RNA content to DNA content. Measurements of RNA:DNA were unsuccessfully attempted for invertebrates.

Data Processing Description

The microplate fluorometer is operated using SoftMax Pro version 5.4 also by Molecular Devices. Raw data were exported to Microsoft Excel for further processing.

Quality control procedure:

Individual samples for which the means were greater than 3 standard deviations from the taxon mean were removed from the data set.

A primary check value was assigned as follows:

1 Perfectly fine

2 Data not evaluated because of too few data points for quality control check

BCO-DMO Processing

BCO-DMO Data Manager Processing Notes:
* Sheet 1 of file "RNA DNA field data.xlsx" (submitted in our online submission system 2023-06-23) was imported into the BCO-DMO data system with values "NA" as missing data values.
** Missing data values are displayed differently based on the file format you download. They are blank in csv files, "NaN" in MatLab files, etc.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* Taxon name and associated LSID for names in this dataset as of 2023-06-23 (source: World Register of Marine Species). Added this list to Methods and Sampling section.
* Date formats converted to ISO 8601.
* Site lat and lon added as data columns from values provided in metadata.

After correspondence with the submitter, "Spotfin mojarro, Eucinostomus melanopterus " in this dataset was updated to "Spotfin mojarra, Eucinostomus argenteus"

Data Files

File
908180_v1_rna-dna-field.csv (Comma Separated Values (.csv), 10.94 KB) MD5:a74ff343f5012257d3bd6de74c0bd6c8 Primary data file for dataset ID 908180, version 1

Supplemental Files

File

Species List
filename: species_list.csv

(Comma Separated Values (.csv), 1.12 KB)
MD5:ae9bd1f0a8ca222367bd84db24f02a2c

Unique species list for data in RNA DNA field data.xslx. World Register of Marine Species Taxa Match performed 2024-01-16 (all exact matches to accepted names as of this date).

Scientific_name, Genus and species in the "Scientific_name" column of this dataset
Common_name, Common name in the "Common_name" column of this dataset
AphiaID, Taxonomic identifier the for the Scientific_name. AphiaID
(see WoRMS)
LSID, Lifescience identifier for the Scientific_name

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2023618

Deployments

None available yet

Instruments

Fluorometer

Supplied Name: Gemini XPS

Supplied Description:

Microplate fluorometer (Molecular Devices, model Gemini XPS). The microplate fluorometer is operated using SoftMax Pro version 5.4 also by Molecular Devices.

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Scientific_name	Scientific name of sample	unitless	species
Common_name	Common name of sample	unitless	common_name
Sample_ID	Sample identifier for a taxon on a sampling date	unitless	sample
Site	location where sample was collected (FAML: pier at in Corpus Christi Channel, Port Aransas, TX, United States, Fisheries and Mariculture Laboratory of the University of Texas Marine Science Institute.; MI: Mud Island in Aransas Bay, TX, United States.)	unitless	site
lat	Site latitude	decimal degrees	lat
lon	Site longitude	decimal degrees	lon
Date_collected	Date sample was collected. ISO 8601 format. Format: %Y-%m-%d	unitless	date
Date_analyzed	Date sample was analyzed. ISO 8601 format. Format: %Y-%m-%d	unitless	date
Tissue	Tissue sampled	unitless	sample_descrip
Primary_check	QC check	unitless	q_flag
RNA_DNA	Ratio of RNA to DNA in sample	unitless	no_bcodmo_term

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Dataset: RNA:DNA measurements - field data