Dataset: Trichodesmium consortia FASTq accessions
Deployment: lab_Webb_Hutchins_Fu

NCBI accession numbers for raw RNA-seq fastq files derived from laboratory-maintained Trichodesmium erythraeum cultures

Principal Investigator:

David A. Hutchins (University of Southern California, USC)

Co-Principal Investigator:

Eric A. Webb (University of Southern California, USC)

BCO-DMO Data Manager:

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

Project:

Adaptation of key N2-fixing cyanobacteria to changing CO2 (HiCO2_AdaptCyano)

Collaborative Research: Iron and phosphorus balanced limitation of nitrogen fixation in the oligotrophic ocean (TriCoLim)

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/726907/data

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Description

These data were derived from laboratory-maintained Trichodesmium erythraeum cultures and contain accessions and links to raw RNA-seq fastq files in NCBI’s Gene Expression Omnibus, accessible through GEO Series accession number GSE94951. The sample accession numbers corresponding to the low and high CO2 samples from this work are GSM2492342, GSM2492343, GSM2492344, and GSM2492345.

These data were reported in the paper (Lee et al., 2017)

Methods & Sampling

Dataset acquisition description

Culturing: Cultures of Trichodesmium erythraeum strain IMS101 were maintained at the University of Southern California, Los Angeles, California, USA, in modified Aquil medium with no fixed nitrogen provided. Cultures were grown at 26ºC in a light:dark cycle of 12:12, and maintained under 120 µmol photons per m^2 s^-1.

Samples GSM2492342 and GSM2492343 were grown as noted above, but under 380 µatm CO2.

Samples GSM2492344 and GSM2492345 were grown as noted above, but under 800 µatm CO2.

Sampling: Cultures were filtered onto 5 µm polycarbonate filters during the middle of the photoperiod, flash frozen, and stored in liquid nitrogen until RNA extraction.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing Notes:
- created a table with a conventional header with dataset name, PI name, version date
- records were compiled from NCBI website; accessions obtained from (Lee et al., 2017).
- hyperlink were created to the NCBI accessions pages.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1260233	NSF Division of Ocean Sciences
OCE-1657757	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Illumina Hi-Seq

Supplied Description:

Used to sequence the extracted RNA, performed at UC San Diego Institute for Genomic Medicine

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
organism_community	host organism from which the microbial community genomic material was extracted	unitless	taxon
pCO2	CO2 level of culture	microatmospheres	pCO2
BioSample	NCBI BioSample accession number: descriptive information about the physical biological materials	unitless	accession_number
SRA	NCBI Sequence Read Archive accession number	unitless	accession_number
GSM	NCBI sample Gene Expression Omnibus accession number	unitless	accession_number
GSM_link	link to NCBI BioSample (GSM) accession webpage for the GSM	unitless	external_link

Database

Contribute Data

Dataset: Trichodesmium consortia FASTq accessions
Deployment: lab_Webb_Hutchins_Fu

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Trichodesmium consortia FASTq accessionsDeployment: lab_Webb_Hutchins_Fu

Dataset acquisition description

Dataset Processing Description

Dataset: Trichodesmium consortia FASTq accessions
Deployment: lab_Webb_Hutchins_Fu