Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Photobacterium profundum

ABSTRACT: Gene expression analysis of Photobacterium profundum DB110 and TW30 toxR mutant strain at 0.1 MPa and 28 MPa

PROVIDER: PRJNA167564 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR500950.fastq.gz	Fastqsanger.gz
	SRR500951.fastq.gz	Fastqsanger.gz
	SRR500952.fastq.gz	Fastqsanger.gz
	SRR500953.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Gene expression analysis of Photobacterium profundum DB110 and TW30 toxR mutant strain at 0.1 MPa and 28 MPa

Project description:Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of wild type (DB110) and toxR (TW30) mutant strains of the deep-sea bacterium Photobacterium profundum. ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae and able to regulate numerous genes involved in virulence. In P. profundum the abundance and activity of the same protein is influenced by hydrostatic pressure and is able to regulate genes in a pressure-dependent manner. To better characterize the ToxR regulon, we have compared the genes differentially expressed in response to pressure changes with those whose expression is altered between wild type and toxR mutant strains. Four samples were analyzed: DB110 strain grown at 0.1 MPa, DB110 strain grown at 28 MPa, TW30 strain grown at 0.1 MPa, TW30 strain grown at 28 MPa. Two independent coltures (replicates) were grown for each sample, RNA was extracted from each replicate and RNAs from the two replicates were pooled together to reduce biological variability. No replicates were included in experimental design.

2012-12-22 | E-GEOD-38259 | biostudies-arrayexpress

Comparative genomic hybridization of Photobacterium profundum DSJ4 genomic DNA vs P profundum SS9 genomic DNA

Project description:Genomic DNA extracted from two different Photobacterium profundum strains: SS9 strain (completely sequenced and used to made the microarray) and DSJ4 strain were labeled with Cy3 and Cy5 fluorophores and competitively hybridized on the microarray built on the basis of the SS9 strain genomic sequence. Aim: the identification of the genomic regions absent in the DSJ4 strain with respect to the SS9 strain. The SS9 strain was isolated from the Sulu Trench and display an optimum growth at 28 MPa (2800 metres of depth). The DSJ4 strain was recovered from a sediment sample obtained from the Ryukyu Trench (Japan) at a depth of 5110 m and displays an optimum growth at 10 MPa (but shows no significant change in growth at pressure up to 50 MPa).

2006-05-25 | E-MEXP-376 | biostudies-arrayexpress

Comparative genomic hybridization of Photbacterium profundum 3TCK genomic DNA vs P profundum SS9 genomic DNA

Project description:Genomic DNA extracted from two different Photobacterium profundum strains: SS9 strain (completely sequenced and used to made the microarray) and 3TCK strain were labeled with Cy3 and Cy5 fluorophores and competitively hybridized on the microarray built on the basis of the SS9 strain genomic sequence. Aim: the identification of the genomic regions absent in the 3TCK strain with respect to the SS9 strain. The SS9 strain was isolated from the Sulu Trench and displays an optimum growth at 28 MPa (2800 metres of depth). The 3TCK strain was isolated from a coastal sample collected near San Diego, California and has an optimum growth at 0.1 MPa.

2006-05-24 | E-MEXP-375 | biostudies-arrayexpress

Gene expression analysis of Photobacterium profundum DB110 and TW30 toxR mutant strain at 0.1 MPa and 28 MPa

2012-12-22 | GSE38259 | GEO

Transcription profiling of Photobacterium profundum SS9 strain cells grown at two different pressure conditions 45 MPa and at 28 MPa

Project description:P. profundum SS9 strain cells were grown at two different pressure conditions 45 MPa and at 28 MPa. RNA extracted from the two different cultures was labelled with Cy5 and Cy3 and competitively hybridized on the same slide.

2006-05-24 | E-MEXP-374 | biostudies-arrayexpress

Transcription profiling of Phytobacterium profundum SS9 strain cells grown at two different pressure conditions 0.1 MPa and at 28 MPa

Project description:P. profundum SS9 strain cells were grown at two different pressure conditions 0.1 MPa and at 28 MPa. RNA extracted from the two different cultures was labelled with Cy5 and Cy3 and competitively hybridized on the same slide.

2005-07-28 | E-MEXP-210 | biostudies-arrayexpress

Exiguobacterium profundum

Project description:Exiguobacterium profundum overview

| PRJNA735816 | ENA

pressure effect on P.profundum proteome

Project description:Photobacterium profundum SS9 total extract digest

2013-06-19 | PRD000619 | Pride

Exiguobacterium profundum strain:TSS-3

Project description:Exiguobacterium profundum strain:TSS-3 Genome sequencing

| PRJNA887767 | ENA

Ecotype diversity and conversion in Photobacterium profundum strains.

Project description:Photobacterium profundum is a cosmopolitan marine bacterium capable of growth at low temperature and high hydrostatic pressure. Multiple strains of P. profundum have been isolated from different depths of the ocean and display remarkable differences in their physiological responses to pressure. The genome sequence of the deep-sea piezopsychrophilic strain Photobacterium profundum SS9 has provided some clues regarding the genetic features required for growth in the deep sea. The sequenced genome of Photobacterium profundum strain 3TCK, a non-piezophilic strain isolated from a shallow-water environment, is now available and its analysis expands the identification of unique genomic features that correlate to environmental differences and define the Hutchinsonian niche of each strain. These differences range from variations in gene content to specific gene sequences under positive selection. Genome plasticity between Photobacterium bathytypes was investigated when strain 3TCK-specific genes involved in photorepair were introduced to SS9, demonstrating that horizontal gene transfer can provide a mechanism for rapid colonisation of new environments.

| S-EPMC4019646 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data