Rhizosphere metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB35738 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This dataset contains the transcriptome sequence of Zostera marina as produced by Illumina sequencing. Four tissues were sequenced, female flower in late and early stages of development, the male flower, the root and leaf tissue.
2016-01-16 | GSE67579 | GEO
Project description:This dataset contains the transcriptome sequence of Zostera marina as produced by Illumina sequencing. Four tissues were sequenced, female flower in late and early stages of development, the male flower, the root and leaf tissue. Full transcriptome sequencing of four tissues, including female flower at two time points in development
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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Zostera marina tissues (including leaves, flowers, roots and rhizoids). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study. Small RNA libraries were derived from leaves, flowers, roots and rhizoids of Zostera marina. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Kayti Tigani for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
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Project description:The bacteria Cobetia marina is globally distributed in different oceanic ecosystems and is able to grow in a wide range of temperatures from 0°C to 41°C, with an optimal growth temperature close to 35°C. Its remarkable characteristics include its ability to form biofilm, produce biosurfactants, and use petroleum-derived hydrocarbons as energy and carbon source. In this context, Cobetia marina is a model for biofilm production and the production of diverse biomolecules of relevance for human and animal health, as well as for environmental protection and recovery. This dataset shows the differential expression of genes and gene regulatory circuits that explain the adaptation of Cobetia marina to different temperatures, serving as a model of evolution in response to selection pressures such as temperature changes in the marine environment. In this study, Cobetia marina was grown at 16°C, 35°C, 38°C, and 41°C to establish differential gene expression using high-throughput RNA sequencing.
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