Dataset: Alteromonas ancestor

Name: Accessions for clones of heterotrophic "helper" bacterium Alteromonas EZ55 grown at elevated and ambient CO2.
Published: 2018-05-09
Keywords: biota, oceans

Cite This Dataset

Project:

Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2 (P-ExpEv)

Program:

Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA)

Principal Investigator:

Sonya T. Dyhrman (Lamont-Doherty Earth Observatory, LDEO)

Co-Principal Investigator:

James Jeffrey Morris (University of Alabama at Birmingham, UA/Birmingham)

Scientist:

Gwenn Hennon (Lamont-Doherty Earth Observatory, LDEO)

BCO-DMO Data Manager:

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

Version:

Version Date:

2018-05-09

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Accessions for clones of heterotrophic "helper" bacterium Alteromonas EZ55 grown at elevated and ambient CO2.

Abstract:

This dataset includes a link to Alteromonas/Prochlorococcus clone NCBI BioProject "Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2", and a listing of the associated FASTQ files. PRJNA377729: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729

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Description

This dataset includes a link to Alteromonas/Prochlorococcus clone NCBI BioProject "Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2", and a listing of the associated FASTQ files.
PRJNA377729 : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729

These data were published in:
Hennon et al. “The impact of elevated CO2 on Prochlorococcus and microbial interactions with 'helper' bacterium Alteromonas” (2018) ISME. Supplemental Table 4

Methods & Sampling

Six clones of high light II Prochlorococcus VOL4, a streptomycin-resistant derivative of strain MIT9312 were isolated by dilution to extinction in Pro99 media pretreated with the helper bacterium Alteromonas sp. strain EZ55. Prochlorococcus clones were made axenic by addition of streptomycin. For co-culture experiments, Alteromonas bacteria were introduced to Prochlorococcus cultures prior to growth experiments. Alteromonas was diluted onto YTSS agar plates and each Prochlorococcus culture was inoculated with a single separate colony. Alteromonas stock cultures were grown in YTSS liquid medium and cryopreserved in 20% glycerol at -80 C.

Each of the six Alteromonas clones from co-culture experiments was grown axenically in ambient or elevated CO2 in co-culture with Alteromonas, in PEv media.

RNA extractions were performed with the RNeasy Mini Kit.

Data Processing Description

Sequence reads were de-multiplexed and trimmed to remove sequencing barcodes. Trimmed reads were aligned to the draft EZ55 genome (Genbank accession SRX022631)) using bowtie2 with sensitive end-to-end mode. Reads aligning to the EZ55 draft genome were counted with HT-seq count.

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- added links to NCBI BioProject page

Data Files

File
Alteromonas_accessions.csv (Comma Separated Values (.csv), 4.04 KB) MD5:6738ebdae9518d094a7c399f717a6e96 Primary data file for dataset ID 735669

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1314336

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Dyhrman_2013		2013-01-01	LDEO	Sonya T. Dyhrman (Principal Investigator)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA)

Supplied Description:

Used to prepare the mRNA libraries. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).

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
bioproject_accession	NCBI BioProject accession number; a collection of biological data related to a single initiative	unitless	accession_number
bioproject_link	url for collection of biological data related to a single initiative	unitless	external_link
biosample_accession	NCBI BioSample accession number	unitless	accession_number
library_ID	short unique identifier for the sequencing library	unitless	sample
title	BioSample title	unitless	sample
library_layout	Paired-end or Single	unitless	no_bcodmo_term
platform	type of DNA sequencing instrument	unitless	instrument
instrument_model	model of DNA sequencer	unitless	inst_model
design_description	description of the methods used to create the sequencing library	unitless	sampling_method
filetype	type of file: FASTQ	unitless	no_bcodmo_term
filename	FASTQ file name	unitless	file_name
filename2	additional FASTQ filename	unitless	file_name
library_strategy	type of sequencer used	unitless	no_bcodmo_term
library_source	sequencing location	unitless	no_bcodmo_term
library_selection	library preparation kit used	unitless	no_bcodmo_term

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Database

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Dataset: Alteromonas ancestor