Dataset: Metadata for RNASeq of green crabs in the northeast Pacific

Name: Metadata for RNASeq of green crabs collected in the northeast Pacific from Apr 2017 to Aug 2021
Published: 2025-01-28
Keywords: Carcinus maenas, genomics, marine invasion, biota, oceans

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Spatial Extent: N:50.698395 E:-122.45115 S:43.35635 W:-127.579577

Coastal northeastern Pacific in the range of Carcinus maenas, from California to British Columbia

Temporal Extent: 2017-04-29 - 2021-08-12

Project:

Collaborative Research: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator (West Coast Carcinus)

Principal Investigator:

Carolyn Tepolt (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Emily Grason (Sea Grant, WSG)

Patrick McDonald (University of Washington, UW)

BCO-DMO Data Manager:

Audrey Mickle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2025-01-28

Restricted:

Validated:

Current State:

Preliminary and in progress

Metadata for RNASeq of green crabs collected in the northeast Pacific from Apr 2017 to Aug 2021

Abstract:

This project explores genomic changes in the invasive European green crab (Carcinus maenas) in the northeast Pacific. It tracks the earliest stages of green crab invasion into a new environment where the species is predicted to have substantial ecological and economic impacts. Samples span time and space across the species range in the northeast Pacific, with a focus on areas where the species is currently expanding. This dataset includes individual metadata for 127 raw RNA-Seq reads, archived at GenBank's SRA under BioProject PRJNA1170986.

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Methods & Sampling

Samples of Carcinus maenas (urn:lsid:marinespecies.org:taxname:107381) were collected by large network of collaborators, usually by trapping but approaches vary. Heart tissue was dissected from crabs after severing the ventral nerve cord, and hearts were preserved in RNALater and frozen at -80 prior to extraction. Total RNA extraction was conducted with TRI reagent and 1-bromo-3-chloropropane. mRNA libraries were prepared with Illumina TruSeq Stranded mRNA kits and individually single-indexed with Illumina index sets A and B. Samples were multiplexed 24 / lane of 150 bp pe Illumina HiSeq4000 sequencing at Azenta (formerly Genewiz; South Plainfield NJ).

Problems/Issues

Some latitude, longitude, and collector information was not reported. Those values are represented as blanks.

Data Processing Description

Samples were demultiplexed by Azenta (formerly Genewiz; South Plainfield NJ), and are provided raw with no further processing.

BCO-DMO Processing

- Imported "BCO-DMO_RNASeq_metadata_NSF-1850996.csv" into the BCO-DMO system
- Converted date field to ISO UTC format YYYY-MM-DD
- Replaced non-standard character '’' with '''
- Exported file as "949682_v1_green_crabs_rna_seq.csv"

Accepted species identifier confirmed on 2025-01-29.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1850945
NSF Division of Ocean Sciences	OCE-1850996

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq4000 sequencers

Supplied Description:

Samples were sequenced using Illumina HiSeq4000 sequencers by Azenta (formerly Genewiz; South Plainfield NJ).

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_name	Individual sample ID	unitless	sample
SRA_accession	SRA accession number for individual sequence files	unitless	SRA_run
biosample_accession	Individual NCBI BioSample code	unitless	BioSample
embayment	General coastal water body from which sample was collected	unitless	site
site	More specific data on collection location provided by collector	unitless	site
state	US state or Canadian province where samples was collected	unitless	region
sex	Sex (M=Male, F=Female, or U=Unknown)	unitless	sex
size_CW	Carapace width of crab in mm	Millimeters (mm)	width
color	Color of ventral side of cephalothorax, as determined by collector	unitless	sample_descrip
collection_date	Date of collection Format: %Y-%m-%d	unitless	date
latitude	Latitude of collection; positive values = North	decimal degrees	lat
longitude	Longitude of collection; positive values = East	decimal degrees	lon
collector	Person who collected the sample	unitless	person
collector_affiliation	Organization through which the sample was collected	unitless	sample_descrip

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Database

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Dataset: Metadata for RNASeq of green crabs in the northeast Pacific