|Thamatrakoln, Kimberlee||Rutgers University (Rutgers IMCS)||Principal Investigator|
|Allen, Andrew E||J. Craig Venter Institute (JCVI)||Co-Principal Investigator|
|Copley, Nancy||Woods Hole Oceanographic Institution (WHOI BCO-DMO)||BCO-DMO Data Manager|
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.
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.
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
|BioProject_type||NCBI BioProject type||unitless|
|BioProject_id||NCBI BioProject identifier||unitless|
|BioSample||NCBI BioSample identifier||unitless|
|Sample_name||NCBI Sample identifier||unitless|
|SRA_id||NCBI SRA identifier||unitless|
|Package_type||NCBI Package type||unitless|
|CTD_cast||CTD cast number||unitless|
|Lat||latitude; north is positive||decimal degrees|
|Long||longitude; east is positive||decimal degrees|
|Date_collection||date of collection; formatted as yyyy-mm-dd||unitless|
|depth_m||depth of sample||meters|
|Dataset-specific Instrument Name|| |
Illumina HiSeq platform
|Generic Instrument Name|| |
Automated DNA Sequencer
|Generic Instrument 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.
R/V Point Sur
|Start Date|| |
|End Date|| |
Cruise DOI: 10.7284/903425
This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database. 2020-02-23 10:58:32