Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Marine gamma proteobacterium HTCC2080

ABSTRACT: Collected from surface waters of the Newport Oregon area of the Coastal Pacific Ocean

PROVIDER: PRJNA18487 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	AAVV01.dat.gz	Other
	AAVV01.fasta.gz	Fasta.gz
	AAVV01.master.dat	Other
	AAVV01.dat.gz	Other

Items per page:

1 - 4 of 4

Similar Datasets

marine gamma proteobacterium HTCC2143

Project description:This marine bacterium was collected from the coastal region of Newport, Oregon.

| PRJNA13605 | ENA

Detection and mapping of species and strains from the diatom genus Pseudo-nitzchia (Bacillariophyceae) along the Oregon and Washington coast using microarray-based, field-deployable, rapid, high-resolution assay

Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition. Total DNA was isolated from 9 Pseudo-nitzschia laboratory cultures and 35 environmental water samples collected during 7 field campaigns in 2007-2009. The environmental samples were collected at distances of 5 to 55 km from the coast, along the following transects in the Pacific Ocean covering over 300 km of the coastline: La Push (LP), Grays Harbor (GH), Columbia River (CR), and Newport Hydroline (NH). The DNA samples were subjected to PCR amplification with the primers specific for ITS1 sequences. The resultant biotin-labeled target samples were analyzed using microarray hybridization with the CombiMatrix ElectraSense 4X2K format. Out of 44 analyzed samples, 40, 2, and 2 were used for single, duplicate and triplicate hybridizations, respectively.

2012-05-31 | E-GEOD-27141 | biostudies-arrayexpress

Rhodobacteraceae bacterium HTCC2083

Project description:This strain was collected in the coastal area near Newport, Oregon.

| PRJNA13508 | ENA

Maribacter sp. HTCC2170

Project description:This strain was collected from the coastal area of Newport, Oregon.

| PRJNA13595 | ENA

Gene Expression in Prokaryotic Microbial Assemblages Across Salinity Gradients in the Columbia River Coastal Margin

Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212). Total RNA was isolated from 64 filtered environmental water samples collected in the Columbia River coastal margin during 4 research cruises (14 from August, 2007; 17 from November, 2007; 18 from April, 2008; and 16 from June, 2008), and analyzed using microarray hybridization with the CombiMatrix 4X2K format. Microarray targets were prepared by reverse transcription of total RNA into fluorescently labeled cDNA. All samples were hybridized in duplicate, except samples 212 and 310 (hybridized in triplicate) and samples 336, 339, 50, 152, 157, and 199 (hybridized once). Sample location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; AST and HAM, Columbia River estuary locations near Astoria (river mile 7-9) and Hammond (river mile 5), respectively; TID, Columbia River estuary locations in the tidal basin (river mile 22-23); BA, river location at Beaver Army Dock (river mile 53) near Quincy, Oregon; UP, river location at mile 74.

2010-09-10 | E-GEOD-18303 | biostudies-arrayexpress

2012-06-01 | GSE27141 | GEO

beta proteobacterium KB13

Project description:This strain was collected from the surface waters of Kaneohe Bay, Hawaii.

| PRJNA13602 | ENA

Rhodobacterales bacterium HTCC2177

Project description:This strain was collected in the coastal region near Newport, Oregon.

| PRJNA13613 | ENA

Lentisphaera araneosa HTCC2155

Project description:This marine bacterium was isolated in the coastal Pacific Ocean near Newport, Oregon.

| PRJNA13437 | ENA

Rhodobacterales bacterium HTCC2255