Dataset: Trichodesmium consortia FASTq accessions

Name: NCBI accessions for raw RNA-seq fastq in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California: deep metatranscriptomic sequencing of Trichodesmium enrichment cultures (HiCO2_AdaptCyano project)
Published: 2018-02-14
Keywords: biota, oceans

Cite This Dataset

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)

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)

Version Date:

2018-02-14

Restricted:

Validated:

Yes

Current State:

Final no updates expected

NCBI accessions for raw RNA-seq fastq in 380 and 750 uatm CO2 from experiments conducted at the University of Southern California: deep metatranscriptomic sequencing of Trichodesmium enrichment cultures (HiCO2_AdaptCyano project)

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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

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

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.

Data Files

File
Tricho_FASTq_accessions.csv (Comma Separated Values (.csv), 719 bytes) MD5:81cde9e6505eb560d97a578d4adf3b23 Primary data file for dataset ID 726901

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
lab_Webb_Hutchins_Fu		2011-08-15	Webb-Hutchins-Fu USC		data info

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

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

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

Status message

Database

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Dataset: Trichodesmium consortia FASTq accessions