Dataset: Metadata for longread sequencing of Carcinus maenas

Name: Metadata for longread sequencing of Carcinus maenas collected from Buzzards Bay, Massachusetts from May 2022 to Aug 2022
Published: 2025-01-29
Keywords: Marine invasion, Carcinus maenas, genomics, biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.949666.1

Spatial Extent: N:41.775408 E:-70.589905 S:41.30566 W:-71.201019

Buzzards Bay, Massachusetts, USA

Temporal Extent: 2022-05-18 - 2022-08-08

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)

BCO-DMO Data Manager:

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

Version:

Version Date:

2025-01-29

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Metadata for longread sequencing of Carcinus maenas collected from Buzzards Bay, Massachusetts from May 2022 to Aug 2022

Abstract:

This project explores genomic changes in the invasive European green crab (Carcinus maenas), including at a putative inversion polymorphism. To begin to explore structural variation without a reference genome, we conducted semi-targeted longread sequencing of the C. maenas genome using MinION sequencing. This dataset includes individual metadata for 6 raw MinION reads, archived at GenBank's SRA under BioProject PRJNA1171011. This sequencing was conducted using crabs from Massachusetts waters.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2025-01-29	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.949666.1	2025-02-11

Methods & Sampling

Samples of Carcinus maenas (urn:lsid:marinespecies.org:taxname:107381) were collected between May 2022 and Aug 2022 from Massachusetts waters.

Extractions were performed with an NEB Monarch HMW DNA Extraction Kit for Cells & Blood (May runs; low success) or a Circulomics Nanobind Tissue Big DNA kit (June and August runs; good success). Library prep was performed with a Oxford Nanopore Cas9 sequencing kit and custom Cas9 probes targeting putative inversion regions. May and June runs used the same first-round set of probes, while August runs used an updated second-round set of probes. Probe sequences are included in the supplemental file and can be cross-referenced using the probe_set value, though targeting is imperfect so much of the data simply reflect non-targeted genome sequencing. Libraries were sequenced on a single flowcell of an Oxford Nanopore MinION mk1c. For each round of sequencing (May, June, and August), the same library was run twice for 24 hours each time, with a flowcell flush at 24 hours. The run_day value captures this, listing this pre- and post-flush runs as run_days 1 and 2, respectively, for each single sample.

Problems/Issues

First round of sequencing (May) resulted in few usable sequences on account of low HMW DNA yield. Samples were collected in Buzzards Bay, MA; precise sample collection coordinates are not known.

Data Processing Description

Minimal initial processing with standard Oxford Nanopore MinKNOW software (v22.03.06) was used to convert native fast5 files into fastq format for downstream processing. Only the fastq files in the "pass" bin were shared to the SRA. The MinKNOW software includes the following subpackage versions: MinKNOW core v5.0.0, Guppy v6.0.7, Bream v7.0.9, and Script Configuration v5.0.8.

BCO-DMO Processing

- Imported "BCODMO_MinION_metadata_NSF-1850996.csv" into BCO-DMO system
- Converted "Collection_date" and "sequencing_date" to ISO 8601 format
- Exported resource as "949666_v1_longread_seq_metadata.csv"

Accepted species identifier confirmed on 2025-01-29.

Data Files

File
949666_v1_longread_seq_metadata.csv (Comma Separated Values (.csv), 796 bytes) MD5:d3b60996bc3078cfa12587bda10556af Primary data file for dataset ID 949666, version 1

Supplemental Files

File

CRISPR-Cas9 crRNA probes to target longread sequencing
filename: BCO-DMO_Cas9-probe-seqs_NSF-1850996.csv

(Comma Separated Values (.csv), 2.05 KB)
MD5:d4b438e23efff3eec0a3330eb172f2ff

Round 1 samples were targeted with probes in round 1, while Round 2 samples (August) were targeted with probes in both rounds 1 and 2.

probe_name: unique probe name
probe_set: round 1 or 2
target_sequence: DNA sequence to be targeted for CRISPR-Cas9 cutting
Cas9_crRNA_probe_sequence: complete CRISPR-Cas9 crRNA sequence to guide cutting

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

Nanopore Sequencer

Supplied Name: Oxford Nanopore MinION mk1c.

Supplied Description:

Sequencing was done with an Oxford Nanopore MinION mk1c.

Instrument Type

Generic Name: Nanopore Sequencer

Generic Description:

A proprietary high-throughput DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence DNA molecules as they pass through nanopores, driven by electrophoresis.

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
Collection_date	Date of collection Format: %Y-%m-%d	unitless	date
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
state	US state or Canadian province where samples was collected	unitless	region
sex	Sex (M=Male, F=Female, or U=Unknown)	unitless	sex
life_stage	Stage of life of sampe (Adult)	unitless	stage
run_ID	Unique identifier for MinION run	unitless	exp_id
sequencing_date	Date that first sequencing run was started Format: %Y-%m-%d	unitless	date
run_day	For a single sample, whether the data were collected on day 1 or 2 of sequencing, where a flow-cell flush was performed in between	days	time_elapsed
probe_set	Set of Cas9 probes used to target sequencing (see additional file in this dataset)	unitless	exp_id