Dataset: Thaumarchaea transcriptomes

Name: Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification.
Published: 2018-07-10
Keywords: oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.739636.1

Spatial Extent: N:38.57506 E:-76.070137 S:38.57506 W:-76.070137

Project:

Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea (AmoA Archaea)

Principal Investigator:

Christopher Dupont (J. Craig Venter Institute, JCVI)

Co-Principal Investigator:

Alyson E. Santoro (University of California-Santa Barbara, UCSB)

Contact:

Christopher Dupont (J. Craig Venter Institute, JCVI)

BCO-DMO Data Manager:

Hannah Ake (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2018-07-10

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification.

Abstract:

Nitrosopelagicus brevis CN25 and U25 were grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2018-07-10	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.739636.1	2019-11-20

Description

Nitrosopelagicus brevis CN25 and U25 were grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing.

Methods & Sampling

Thaumarchaea transcriptomes sequences.

Data Processing Description

Libraries were sequenced in one 300 cycle NextSEQ run. Raw Illumina reads in fastq format are interleaved to match paired ends. Sequencing primers and barcode indexes were identified by BLAST against the NCBI vector database and trimmed along with regions with Q scores < 30. Reads mapping to ribosomal RNAs were identified and removed using ribopicker.

Reads were mapped (clc_ref_assemble_long –s 0.9, CLC genomics) to the Ca. N. brevis strains CN25 or U25 genome sequences. Raw read counts per open reading frame (ORF) were compiled.

BCO-DMO Data Processing Notes:

- Included links to NCBI via accession numbers
- Reformatted column names to comply with BCO-DMO standards

Data Files

File
accessions.csv (Comma Separated Values (.csv), 2.84 KB) MD5:6e045bed251d5f73a98fd794b7d192ad Primary data file for dataset ID 739636

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1260006
NSF Division of Ocean Sciences	OCE-1259994

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina NextSEQ 500

Supplied Description:

Used to identify samples

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
Accession	Accession number and NCBI link	unitless	accession_number
Sample_Name	Sample name	unitless	sample
Organism	Species of organism	unitless	species
Tax_ID	Taxonomic identification	unitless	sample
Strain	Strain identification	unitless	sample