Dataset: RNASeq Exp5

Name: Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri (Iron regulation in Vibrio project)
Published: 2013-11-21
Keywords: oceans

Cite This Dataset

Project:

Iron limitation, carbon metabolism and siderophore production in marine bacteria - a systems biology approach (Iron regulation in Vibrio)

Principal Investigator:

Dr Elizabeth Mann (Skidaway Institute of Oceanography, SkIO)

Co-Principal Investigator:

Dr Eric Stabb (University of Georgia, UGA)

Dr Eberhard Voit (Georgia Institute of Technology, GA Tech)

BCO-DMO Data Manager:

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

Version Date:

2013-11-21

Validated:

Yes

Current State:

Final no updates expected

Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri (Iron regulation in Vibrio project)

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Description

An RNA-Seq experiment was performed in order to define the regulon of the small, regulatory RNA RyhB in Vibrio fischeri ES114. This was done by comparing the global gene expression in wildtype and ryhB mutant strains of V. fischeri. Since RyhB is de-repressed only under iron limiting conditions, this comparison must be performed when the level of intracellular iron is low.

Methods & Sampling

Wildtype and mutant ryhB strains of ES114 were grown in Aquil media with glucose and NH4 as carbon and nitrogen sources, respectively. Parallel cultures of each strain were resuspended in media containing low iron and followed until the growth rates decreased. At this point, samples for RNA were collected by filtration, stored in RNAlater and later extracted using standard methods. rRNA depleted cDNA libraries were submitted to UGA’s Georgia Genomics Center for sequencing on an Illumina MiSeq instrument.

Data Processing Description

Base quality and trimming of reads was assessed using the FastX-Toolkit v0.0.13.2, only reads above a Q30 value were retained. Reads were mapped back to the Vibrio fischeri reference genome using TopHat v1.2.0. Expressed genes and transcripts were assembled for each replicate culture separately using Cufflinks v2.1.1. Cuffmerge v.2.1.1 was then utilized to merge all assemblies from the wildtype and ryhB mutant cultures, respectively. Finally, differentially expressed genes were identified using Cuffdiff v2.1.1.

Data Files

File
Vibrio_RNASeq5.csv (Comma Separated Values (.csv), 23.20 KB) MD5:f5342a6bd8280dc915e34124d7731542 Primary data file for dataset ID 471914

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0929203

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Automated Sequencer

Supplied Description:

Illumina MiSeq

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
gene_function	gene function: specific category	unitless	no_bcodmo_term
gene_name	gene name	unitless	no_bcodmo_term
gene_identifier	The VF_#### code includes a code for the particular organism (VF=Vibrio fischeri) and the gene's location (e.g. VF_0619 and VF_0620 will be adjacent genes)	unitless	no_bcodmo_term
predict_bind	Genes marked with a "P" have a predicted RyhB binding site identified by the programs sTarPicker or TargetRNA	unitless	no_bcodmo_term
FPKM_RyhB	RyhB mutant fragments per kilobase of gene per million fragments mapped	fragments/kilobase/million fragments mapped	no_bcodmo_term
FPKM_WT	wild type mutant fragments per kilobase of gene per million fragments mapped	fragments/kilobase/million fragments mapped	no_bcodmo_term
FPKM_RyhB_WT	ratio of RyhB to wild type	unitless	no_bcodmo_term
Log2_FPKM_RyhB_WT	log base 2 of ratio	unitless	no_bcodmo_term
p_value	probability of significance	unitless	no_bcodmo_term

Status message

Database

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Dataset: RNASeq Exp5