Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1277248 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33987400_1.fastq.gz | Fastqsanger.gz | |||
| SRR33987400_2.fastq.gz | Fastqsanger.gz | |||
| SRR33987401_1.fastq.gz | Fastqsanger.gz | |||
| SRR33987401_2.fastq.gz | Fastqsanger.gz | |||
| SRR33987402_1.fastq.gz | Fastqsanger.gz |
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Project description:Expression diversity of P. ramorum isolates belonging to the NA1 clonal lineage growing on solid CV8 was examined. It was found that although all the analyzed isolates belonged to a single clonal lineage, expression patterns were distinctive between isolates originating from coast live oak and California bay laurel.
2012-03-01 | GSE36178 | GEO
Project description:Due to difficulties inherent in designating conservation units for effective species management and conservation, the use of multiple complementary sources of information is required to identify and assess the designation of conservation units based on the degree of variation among populations within a species. In this study, we combined estimates of microsatellite and transcriptomic variation to assess the population structure and potential for adaptive variation of threatened Atlantic salmon, Salmo salar, among rivers in the Bay of Fundy. In general, population structure identified by genetic differentiation was consistent with the patterns of variation in gene expression. Both data sets provided clear indication of strong regional differentiation between rivers located within the inner Bay of Fundy relative to rivers located within the outer Bay of Fundy or the Southern Uplands region. There was also support for more refined population structure; there was some differentiation in both microsatellite and gene expression patterns between salmon from rivers in the two regions of the inner Bay of Fundy: Chignecto Bay and Minas Basin. Consistent patterns apparent in the genetic and transcriptomic dataset indicate that Atlantic salmon populations from the inner and outer Bay of Fundy reflect unique genetic lineages, with some evidence of unique genetic legacies between regions of the inner Bay of Fundy, and even between individual rivers within a region. Consistency of the microarray data across two years helps to validate the use of this technique as a useful tool in assessment of variation among wild populations for species conservation. Atlantic salmon samples used in this analysis were collected from Mactaquac and Coldbrook Biodiversity Centres on the east coast of Canada. In year one, eight individuals were hybridized per strain (five strains; 40 individuals in total). This design incorporated dye-swap replicates in which two slides were hybridized with the same pair of individuals, but the dyes were swapped for one of the slides. Therefore, in year one a total of 40 slides were used. Because of the large number of strains assessed in year two (12), dyes were balanced across slides to maximize biological replication. Six individuals were hybridized per strain; three of these were labelled with Cy3, and three were labelled with Cy5 (for a total of 36 arrays in year two).
2010-05-19 | E-GEOD-19111 | biostudies-arrayexpress
Project description:Due to difficulties inherent in designating conservation units for effective species management and conservation, the use of multiple complementary sources of information is required to identify and assess the designation of conservation units based on the degree of variation among populations within a species. In this study, we combined estimates of microsatellite and transcriptomic variation to assess the population structure and potential for adaptive variation of threatened Atlantic salmon, Salmo salar, among rivers in the Bay of Fundy. In general, population structure identified by genetic differentiation was consistent with the patterns of variation in gene expression. Both data sets provided clear indication of strong regional differentiation between rivers located within the inner Bay of Fundy relative to rivers located within the outer Bay of Fundy or the Southern Uplands region. There was also support for more refined population structure; there was some differentiation in both microsatellite and gene expression patterns between salmon from rivers in the two regions of the inner Bay of Fundy: Chignecto Bay and Minas Basin. Consistent patterns apparent in the genetic and transcriptomic dataset indicate that Atlantic salmon populations from the inner and outer Bay of Fundy reflect unique genetic lineages, with some evidence of unique genetic legacies between regions of the inner Bay of Fundy, and even between individual rivers within a region. Consistency of the microarray data across two years helps to validate the use of this technique as a useful tool in assessment of variation among wild populations for species conservation. Atlantic salmon samples used in this analysis were collected from Mactaquac and Coldbrook Biodiversity Centres on the east coast of Canada. In year one, eight individuals were hybridized per strain (five strains; 40 individuals in total). This design incorporated dye-swap replicates in which two slides were hybridized with the same pair of individuals, but the dyes were swapped for one of the slides. Therefore, in year one a total of 40 slides were used. Because of the large number of populations assessed in year two (12), dyes were balanced across slides to maximize biological replication. Six individuals were hybridized per strain; three of these were labelled with Cy3, and three were labelled with Cy5 (for a total of 36 arrays in year two).
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Project description:Here we developed a new high-throughput polymorphism detection and genotyping method based on identifying restriction cut site polymorphisms using a microarray platform. We compared the genomes of 20 individual urchins; 10 from the northern part of the species range (Boiler Bay, OR) and 10 from the southern part of the range (San Diego, CA).
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Project description:Gas hydrates, also known as clathrates, are cages of ice-like water crystals encasing gas molecules such as methane (CH4). Despite the global importance of gas hydrates, their microbiomes remain mysterious. Microbial cells are physically associated with hydrates, and the taxonomy of these hydrate-associated microbiomes is distinct from non-hydrate-bearing sites. Global 16S rRNA gene surveys show that members of sub-clade JS-1 of the uncultivated bacterial candidate phylum Atribacteria are the dominant taxa in gas hydrates. The Atribacteria phylogeny is highly diverse, suggesting the potential for wide functional variation and niche specialization. Here, we examined the distribution, phylogeny, and metabolic potential of uncultivated Atribacteria in cold, salty, and high-pressure sediments beneath Hydrate Ridge, off the coast of Oregon, USA, using a combination of 16S rRNA gene amplicon, metagenomic, and metaproteomic analysis. Methods were developed to extract bacterial cellular protein from these sediments, as outlined below. Sample Description Three sediments samples were collected from beneath Hydrate Ridge, off the coast of Oregon, USA. Sediments were cored at ODP site 1244 (44°35.1784´N; 125°7.1902´W; 895 m water depth) on the eastern flank of Hydrate Ridge ~3 km northeast of the southern summit on ODP Leg 204 in 2002 and stored at -80°C at the IODP Gulf Coast Repository. E10H5 sediment is from 68.5 meters below sediment surface interface C1H2 sediment is from 2 meters below sediment surface interface. C3H4 sediment is from 21 meters below sediment surface interface.
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