Dataset: Microbial eukaryotic focused metatranscriptome data

Name: Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015
Published: 2018-10-15
Keywords: microbial ecology, microbial eukaryotes, metatranscriptomics, protistan trophic strategies, microbial eukaryotic metatranscriptomics, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.745518.2

Spatial Extent: N:33.55 E:-118.4 S:33.55 W:-118.4

Temporal Extent: 2015-05-20

Project:

Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series (SPOT)

Principal Investigator:

David Caron (University of Southern California, USC)

Co-Principal Investigator:

Sarah K. Hu (University of Southern California, USC)

Contact:

Sarah K. Hu (University of Southern California, USC)

BCO-DMO Data Manager:

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

Version:

Version Date:

2018-10-15

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015

Abstract:

Seawater was collected via Niskin bottles mounted with a CTD from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Raw sequence data was generated as part of a metatranscriptome study targeting the protistan community. Raw sequences are available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP110974, BioProject: PRJNA391503). Sequences for BioProject PRJNA608423 will be available at NCBI on Jan 1st, 2021. These data were published in Hu et al. (2018).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2018-10-15	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.745518.2	2020-05-11

Description

These data were published in Hu et al. (2018).

Methods & Sampling

Seawater was collected from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Briefly, seawater was pre-filtered (80 mm) into 20 L carboys to minimize the presence of multicellular eukaryotes. Replicate samples (ranging in volume from 1.5-3.5 L) from each depth were filtered onto sterile GF/F filters (nominal pore size 0.7 mm, Whatman, International Ltd. Florham Park, NJ). While we cannot avoid some impact that sample handling (i.e., bringing samples to the surface) may have had on our results, filters were immediately placed in 1.5 mL of lysis buffer and flash frozen in liquid nitrogen in < 40 min and away from light to minimize RNA degradation.

Total RNA was extracted from each filter using a DNA/RNA AllPrep kit (Qiagen, Valencia, CA, #80204) with an in-line genomic DNA removal step (RNase-free DNase reagents, Qiagen #79254) (dx.doi.org/10.17504/protocols.io.hk3b4yn). Extracted RNA was quality checked and low biomass samples were pooled. Six replicates were processed and sequenced from the surface, while pairs of filters were pooled for either 150 or 890 m, yielding 3 and 4 replicates respectively (Supporting Information Table S1). RNA concentrations were normalized before library preparation (Supporting Information). ERCC spike-in was added before sequence library preparation with Kapa’s Stranded mRNA library preparation kit using poly-A tail selection beads to select for eukaryotic mRNA (Kapa Biosystems, Inc., Wilmington, MA, #KK8420).

Also see:

https://www.protocols.io/view/sample-collection-from-the-field-for-downstream-mo-hisb4eehttps://www.protocols.io/view/rna-and-optional-dna-extraction-from-environmental-hk3b4yn

The associated assembly files can be found at Zenodo (see Hu, S. K. (2017), DOI: 10.5281/zenodo.1202041). The assembly files were also published in the journal publication Hu, et al. (2018).

Related code can be found in the github repository https://github.com/shu251/SPOT_metatranscriptome. The version of the code used for these publications can be found in the Supplemental Files section of this page.

Data Processing Description

Sequence adapters, low quality (phred score < 10, from 5’ and 3’ ends, and within a 25 bp sliding window) or short sequences (< 50 bps), and sequences containing more than 50 consecutive As or Ts were removed using Trimmomatic v. 0.32 (Bolger et al., 2014). All quality trimmed sequences were aligned to ERCC sequences using ‘align_and_estimate_abun- dance.pl’ in the Trinity v. 2.1.1 (Grabherr et al., 2011) package. Reads that were aligned to ERCC sequences were removed using a custom PERL script (available: https://github.com/shu251/SPOT_metatranscriptome).

BCO-DMO Processing

[Changes discussed with and reviewed by the data submitter]
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values in this dataset are displayed as "nd" for "no data." nd is the default missing data identifier in the BCO-DMO system.
* removed columns "object_status" and blank columns "filename3" and "filename4."
* Added column SRA_ID_link to the SRA run at NCBI
* removed column "assembly" which had values of "See related publication for access to assembly files" This information was included in the Methods & Sampling section of the methodology and further explained.
* For curatorial purposes BCO-DMO forked the github code repository https://github.com/shu251/SPOT_metatranscriptome and created a github release (see https://github.com/BCODMO/SPOT_metatranscriptome/releases/tag/bcodmo_v1). The release .zip file was downloaded to BCO-DMO's servers and added to the dataset landing page as a supplemental file to satisfy NSF OCE sharing requirements.
* changes in version 2: data for bioproject PRJNA608423 added to the dataset.

Data Files

File
metaT.csv (Comma Separated Values (.csv), 11.80 KB) MD5:cbec0cc726f0b64619a035aba3abdbfa Primary data file for dataset ID 745518

Supplemental Files

File

SPOT metatranscriptome code from Github, release bco-dmo_v1
filename: SPOT_metatranscriptome-bcodmo_v1.zip

(ZIP Archive (ZIP), 810.06 KB)
MD5:369ccce50b2d833723c7f9ea7607e78d

Zip file containing required code for data compilation and analysis for a eukaryotic-focused metatranscriptome survey in the North Pacific. This is release "bcodmo_v1" https://github.com/BCODMO/SPOT_metatranscriptome/tree/bcodmo_v1.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1737409

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
SPOT_Yellowfin_Cruises		2005-01-19	R/V Yellowfin		data info

Instruments

Automated DNA Sequencer

Supplied Name: HiSeq

Supplied Description:

HiSeq High Output 125 bp PE sequencing was performed at UPC Genome Core at University of Southern California, Los Angeles, CA (BioProject: PRJNA391503).

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.

Niskin bottle

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
SRA_run	SRA Run identifier at NCBI	unitless	accession_number
SRA_run_link	URL for SRA Run Page at NCBI	unitless	external_link
SRA_study	SRA study identifier at NCBI	unitless	accession_number
bioproject_accession	BioProject accesion number at NCBI	unitless	accession_number
biosample_accession	BioSample accession number at NCBI	unitless	accession_number
library_ID	SRA title	unitless	sample_descrip
title	Descriptive title of SRA accession	unitless	sample_descrip
sample_name	Sample name	unitless	sample_descrip
library_strategy	Library strategy ("AMPLICON")	unitless	sample_descrip
library_source	Library source ("TRANSCRIPTOMIC" or "GENOMIC")	unitless	sample_descrip
library_selection	Library selection ("PCR")	unitless	sample_descrip
library_layout	Library layout ("paired")	unitless	sample_descrip
platform	Sequencing platform ("Illumina")	unitless	sample_descrip
instrument_model	Sequencing instrument model ("Illumina MiSeq")	unitless	sample_descrip
design_description	Sequencing design description	unitless	sample_descrip
filetype	Type of files	unitless	sample_descrip
filename	Name of file 1 (see NCBI for access)	unitless	file_name
filename2	Name of file 2 (see NCBI for access)	unitless	file_name