Dataset: Pro_ancestor
Deployment: Dyhrman_2013

Clones of Prochlorococcus MIT9312 and link to BioProject

Principal Investigator:

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

Co-Principal Investigator:

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

BCO-DMO Data Manager:

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

Project:

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

Data URL:

https://www.bco-dmo.org/dataset-deployment/692265/data

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Description

This dataset includes a link to Prochlorococcus clone NCBI BioProject and associated metadata.
PRJNA377729 : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729

Methods & Sampling

Dataset acquisition description

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 Prochlorococcus clones was grown in ambient or elevated CO2 in co-culture with Alteromonas, in PEv media.

The mRNA libraries were prepared for Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).

RNA extractions were performed with the RNeasy Mini Kit.

Data Processing Description

Dataset Processing Description

Sequence reads were de-multiplexed and trimmed to remove sequencing barcodes. Trimmed reads were aligned to both the MIT9312 gene models (accession: NC_007577.1) and the draft EZ55 genome (Genbank accession TBD) using bowtie2 with sensitive end-to-end mode. Reads aligning to coding sequences in the MIT9312 gene models were counted with samtools idxstats. 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
- replaced blanks with nd (no data)

More information about this dataset deployment

Funding

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

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

Supplied Name	Supplied description	Supplied Units	Standard Name
sample	sequencing facility sample identifier	unitless	sample
sample_title	laboratory sample identifier	unitless	sample_descrip
NCBI_BioProject	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
organism	bacterium used in this study	unitless	taxon
strain	population of organism that descends from a single organism or pure culture isolate	unitless	taxon
isolate	specific individual from which this sample was obtained	unitless	no_bcodmo_term
isolation_source	physical/ environmental/ geographic source of the sample	unitless	no_bcodmo_term
collection_date	date sample was obtained	date	date
geo_loc_name	geographical origin of the sample	unitless	site_descrip
sample_type	sample type such as whole organism, mixed culture, cell culture, metagenomic assembly	unitless	sample_type
biomaterial_provider	laboratory and principal investigator where sample came from	unitless	laboratory
collected_by	laboratory and principal investigator where organism was isolated	unitless	laboratory
lat_lon	geographical coordinates of the location where the sample was collected; north and east are positive	decimal degrees	lat
depth	vertical distance below the surface where sample was collected	meters	depth
env_biome	descriptor of the broad ecological context of sample	unitless	region
genotype	observed genotype	unitless	sample_type
passage_history	number of sample generations	generations	no_bcodmo_term
samp_size	amount of sample collected	number of cells	count
temp_C	temperature at which sample was collected	degrees Celsius	temp
light_level	light level at which sample was collected	micromol photons m-2 s-1	PAR_photons
light_dark_hr	number of hours of light:dark for a 24 hour period	hours:hours	no_bcodmo_term
CO2	carbon dioxide concentration	ppm	pCO2
Alkalinity	buffering capacity of water	umoles/kg	TALK
pH	scale of acidity	unitless	pH
DIC	dissolved inorganic carbon concentration	umoles/kg	DIC
co_cultured_with	additional organisms grown with the primary organism	unitless	no_bcodmo_term
Media	type of water or broth organism was grown in	unitless	no_bcodmo_term

Database

Contribute Data

Dataset: Pro_ancestor
Deployment: Dyhrman_2013

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Pro_ancestorDeployment: Dyhrman_2013

Dataset acquisition description

Dataset Processing Description

Dataset: Pro_ancestor
Deployment: Dyhrman_2013