Dataset: HRR 18S full-length sequence BLAST results
Deployment: PS1809

HRR 18S full-length sequence BLAST results

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/922101

Principal Investigator:

Lisa Campbell (Texas A&M University, TAMU)

Co-Principal Investigator:

Darren W. Henrichs (Texas A&M University, TAMU)

Contact:

Chetan Gaonkar (Texas A&M University, TAMU)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

RAPID: Hurricane Impact on Phytoplankton Community Dynamics and Metabolic Response (HRR)

Version:

Deployment Synonyms:

HRR, PS18-09

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Description

Methods & Sampling

Dataset acquisition description

On September 23, 2017, on HRR cruise Leg 1 (R/V Point Sur PS18-09), samples were collected at 6 stations (S06, S11, S16, S21, SS, and GI) from the surface depth bottle in a CTD rosette. Triplicate 500-1000 milliliter (mL) samples were filtered and immediately fixed in RNALater. Triplicate samples from each station/depth were extracted with AllPrep DNA/RNA MiniKit (Qiagen, USA) following the manufacturer's instructions. DNA concentration and quality were evaluated using a Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA). All the samples extracted for DNA were normalized to 5 nanograms per microliter (ng/µL) concentration for the amplicon library construction.

The full-length 18S rDNA region was amplified using 18S primers (Medlin et al. 1988; Edgar & Theriot 2004). Library construction and amplicon sequencing were performed at the Campbell Lab, Texas A&M University using Oxford Nanopore minION. The output sequencing results as fasta files were deposited in NCBI's GenBank under the project number PRJNA592369.

Data Processing Description

Dataset Processing Description

Fastq files for all six station samples were quality checked using FastQC. Resulting sequences were taxonomically annotated using BLAST search against PR2 database v5.0.0. The BLAST analysis used an assignment approach with similarity was ≥ 90% and query coverage was ≥ 1000 bp against the reference sequence. Any sequence that did not compile with this criterion was not used in this study. The following thresholds for identity with BLAST results were used for taxonomic assignment clustering: genus (95%), family (93%), class (92%), and order (90%). Archaeal and Bacterial sequences were removed from these results.

Additional tools used are:
Oxford Nanopore Technologies. Guppy protocol. Available at: https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview [Accessed 21 Aug 2023].

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1760620	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Oxford Nanopore minION Mk1C

Supplied Description:

Library construction and amplicon sequencing was performed at Campbell Lab, Texas A&M University using Oxford Nanopore minION.

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.

CTD - profiler

Supplied Name: CTD rosette bottle

Supplied Description:

Samples were collected from the surface depth bottle in a CTD rosette.

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

Spectrophotometer

Supplied Name: Nanodrop spectrophotometer

Supplied Description:

DNA concentration and quality were evaluated using a Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA).

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Station	sampling station number	unitless	station
Leg	cruise leg	unitless	leg
Latitude	latitude of sampling station; positive values = North	decimal degrees	lat
Longitude	longitude of sampling station; negative values = West	decimal degrees	lon
Sequence_ID	OTU sequence generated from the HRR data	unitless	sequence
Taxonomy	taxonomic annotation of the O.T.U.	unitless	taxon
Similarity	percentage of identical matches	percent	sample_descrip
length	alignment length (sequence overlap)	base pairs (bp)	length
mismatches	number of mismatches	base pairs (bp)	sample_descrip
gaps	number of gap openings	unitless	sample_descrip
Q_start	start of alignment in query	base pairs (bp)	sample_descrip
Q_end	end of alignment in query	base pairs (bp)	sample_descrip
R_start	start of alignment in reference sequence	base pairs (bp)	sample_descrip
R_end	end of alignment in reference sequence	base pairs (bp)	sample_descrip
e_value	number of expected hits of similar quality	unitless	sample_descrip
score	Bit-score	unitless	sample_descrip
file_name_orig	original name of the csv file for this station+leg	unitless	file_name

Database

Contribute Data

Dataset: HRR 18S full-length sequence BLAST results
Deployment: PS1809

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: HRR 18S full-length sequence BLAST resultsDeployment: PS1809

Dataset acquisition description

Dataset Processing Description

Dataset: HRR 18S full-length sequence BLAST results
Deployment: PS1809