Dataset: DYEatom: Metatranscriptome accessions and assembled contigs
Deployment: PS1312

Principal Investigator:

Kimberlee Thamatrakoln (Rutgers University, Rutgers IMCS)

Co-Principal Investigator:

Andrew E. Allen (J. Craig Venter Institute, JCVI)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Linking physiological and molecular aspects of diatom silicification in field populations (Diatom Silicification)

Deployment Synonyms:

DYEatom

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/768556/data

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Description

Metadata for assembled contigs and ORFS from metatranscriptome analysis from CTD casts in the Monterey Bay area on RV/Point Sur cruise PS1312, June-July 2013.

Methods & Sampling

Dataset acquisition description

Water was collected using Niskin bottles mounted on a CTD rosette. Biomass for metatranscriptomic analysis was collected by filtration (after a 200 micron pre-filtration) onto 47 mm, 1.2-micron pore size polycarbonate filters at <5 psi for no longer than 15 min to minimize degradation. Filters were flash frozen in liquid nitrogen and stored at -80 degrees C. Upon analysis, filters were thawed and RNA was extracted using TRIzol reagent according to the manufacturer’s protocol (Life Technologies). Metatranscriptome libraries were constructed using 500 ng of total RNA and a TruSeq RNA Sample Preparation Kit (Illumina; San Diego, CA) following the Low-Throughput protocol. The mean size of the final libraries was confirmed to be between 359-420 base pairs (bp) using an Agilent Bioanalyzer 2100 (Santa Clara, CA). Libraries were paired-end sequenced (2x150 bp) on the Illumina HiSeq platform. ORFs were annotated via BLASTP alignment (e-value > 10-3) to a comprehensive protein database, phyloDB, as well as screened for function de-novo by assigning Pfams, TIGRfams and transmembrane tmHMMs with hmmer 3.0 (http://hmmer.org/). PhyloDB 1.076 consists of 24,509,327 peptides from 19,962 viral, 230 archaeal, 4,910 bacterial, and 894 eukaryotic taxa. It includes peptides at KEGG, GenBank, JGI, ENSEMBL, CAMERA, and various other repositories, as well as from the 410 taxa of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. Taxonomic annotation of ORFs was also conducted via BLASTP to phyloDB.

All cruise related data are available publicly at the Biological and Chemical Oceanography Data Management Office under project number 550825 (https://www.bco-dmo.org/project/550825). The metatranscriptomic data have been deposited in the NCBI sequence read archive (BioProject accession no. PRJNA528986: BioSample accession nos. SAMN11263616 - SAMN11263639 and SAMN11258802-SAMN11258825). Assembled contigs used in this study can also be found at https://scripps.ucsd.edu/labs/aallen/data/.

Unassembled reads and rRNA data from this study: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA528986
Assembled contigs: See Supplemental Files.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing Notes:
- created flat table from info at GenBank and metadata submitted by PI
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- added cruise_id

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1333929	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq platform

Supplied Description:

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

Supplied Name	Supplied description	Supplied Units	Standard Name
BioProject_type	NCBI BioProject type	unitless	exp_type
BioProject_id	NCBI BioProject identifier	unitless	exp_id
BioSample	NCBI BioSample identifier	unitless	accession_number
Sample_name	NCBI Sample identifier	unitless	sample
SRA_id	NCBI SRA identifier	unitless	sample
Package_type	NCBI Package type	unitless	sample_type
version	NCBI version	unitless	no_bcodmo_term
Accession	NCBI Accession	unitless	accession_number
ID	NCBI ID	unitless	accession_number
cruise_id	cruise identifier	unitless	cruise_id
CTD_cast	CTD cast number	unitless	cast
Lat	latitude; north is positive	decimal degrees	lat
Long	longitude; east is positive	decimal degrees	lon
Date_collection	date of collection; formatted as yyyy-mm-dd	unitless	date
station	station number	unitless	station
depth_m	depth of sample	meters	depth

Database

Contribute Data

Dataset: DYEatom: Metatranscriptome accessions and assembled contigs
Deployment: PS1312

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: DYEatom: Metatranscriptome accessions and assembled contigsDeployment: PS1312

Dataset acquisition description

Dataset Processing Description

Dataset: DYEatom: Metatranscriptome accessions and assembled contigs
Deployment: PS1312