Dataset: Substrate-specific metabolic responses of model marine bacteria

Name: Metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates
Published: 2023-12-06
Keywords: RNA, sequence, bacteria, metabolism, marine, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.916134.1

Temporal Extent: 2022-02-22 - 2022-07-17

Project:

C-CoMP Model Bacteria Physiological Studies (C-CoMP Model Bacteria)

Program:

Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Principal Investigator:

Mary Ann Moran (University of Georgia, UGA)

Scientist:

Zachary Shane Cooper (University of Georgia, UGA)

Data Manager:

Laura Gray (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-12-06

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates

Abstract:

This dataset includes metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002. These model marine bacteria were grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates. The data are sampled so as to capture the metabolic differences the bacteria employ when catabolizing these different substrates and when switching between them. The raw RNA sequences (50 bp reads in fastq format) have been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA972985 (https://www.ncbi.nlm.nih.gov/bioproject/972985).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-12-06	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.916134.1	2023-12-12

Methods & Sampling

This lab study took place in Athens, Georiga (GA), USA within the Department of Marine Sciences at the University of Georgia. Experiments were conducted on several dates: samples ending in _glc_a/b/c (samples grown with glucose only) were collected February 22-23, 2022; samples ending in _ac_a/b/c (samples grown with acetate only) were collected June 24-25, 2022; and the rest of the samples ending with _glc_ac_5/8/19/34_a/b/c (grown with both glucose and acetate) were collected July 16-17, 2022.

Samples were collected for transcriptomic analysis during exponential growth phase from liquid cultures, and samples were pelleted and immediately frozen at -80°C. RNA was extracted from thawed samples using the Zymo Quick-RNA Fungal/Bacterial Microprep kit (Irvine, CA, USA). Ribosomal RNAs were depleted using NEBNext® rRNA Depletion Kit (Ipswich, MA, USA), and the remaining RNA was purified using the Zymo RNA Clean and Concentrator-5 kit (Irvine, CA, USA). RNA concentration was quantified using Qubit fluorometry (Invitrogen, Waltham, MA, USA), and libraries were prepped using the NEBNext® Ultra™ II Directional RNA Library Prep kit (Ipswich, MA, USA). Sequencing was conducted at the Georgia Genomics and Bioinformatics Center (Athens, GA, USA) using the Illumina NextSeq 2000 platform to obtain 50-bp single-end reads.

Data Processing Description

The submitted data are raw RNA sequences in 50 bp reads in fastq format and are otherwise unprocessed. RNA sequences can be accessed on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA972985 (https://www.ncbi.nlm.nih.gov/bioproject/972985).

Within this dataset, transcripts from Ruegeria pomeroyi DSS-3 are included in the Ruegeria pomeroyi DSS-3 Digital Microbe data package that is currently available on the C-CoMP Zenodo Community page (doi: 10.5281/zenodo.7888446).

BCO-DMO Processing

- Imported original file "CCoMPmodelbacteria_metabolicresponses_primarydatafile.csv" into the BCO-DMO system.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "916134_v1_transcriptomic_expression_metadata.csv".

Data Files

File
916134_v1_transcriptomic_expression_metadata.csv (Comma Separated Values (.csv), 4.34 KB) MD5:98986a18324d7463c6fcbca225e7de19 Primary data file for dataset ID 916134, version 1

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2019589

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina NextSeq 2000

Supplied Description:

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.

Fluorometer

Supplied Name: Qubit Fluorometer

Supplied Description:

Instrument Type

Generic Name: Fluorometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/113/

Generic Description:

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Name	Name of sample used during the experiment	unitless	sample
Accession	NCBI BioSample Accession Number	unitless	accession_number
BioProject	NCBI BioProject Accession Number	unitless	BioProject
Organism	Type of model marine bacteria used in this experiment	unitless	taxon
Strain	Strain number for the referenced bacteria	unitless	taxon
Tax_ID	NCBI Taxonomy ID	unitless	taxon
Glucose_initial_concentration_uM	Initial concentration of glucose	micromolar concentration	treatment
Acetate_initial_concentration_uM	Initial concentration of acetate	micromolar concentration	treatment
Sample_description	Description of growth and collection conditions	unitless	sample_descrip