Root metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA756877 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:root metagenome Taxonomy ID: 1118232 Metagenome
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Project description:D-galactose orally intake ameliorate DNCB-induced atopic dermatitis by modulating microbiota composition and quorum sensing. The increased abundance of bacteroidetes and decreased abundance of firmicutes was confirmed. By D-galactose treatment, Bacteroides population was increased and prevotella, ruminococcus was decreased which is related to atopic dermatitis.
2022-04-29 | E-MTAB-11632 | biostudies-arrayexpress
Project description:This study reports the root endophytic microbial community profile in rice (Oryza sativa L.), the largest food crop of Asia, using 16S rRNA gene amplicon sequencing. Metagenome of OS01 and OS04 consisted of 11,17,900 sequences with 300 Mbp size and average 55.6% G + C content. Data of this study are available at NCBI Bioproject (PRJNA360379). The taxonomic analysis of 843 OTU's showed that the sequences belonged to four major phyla revealing dominance of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria. Results reveal the dominance of Bacillus as major endophytic genera in rice roots, probably playing a key role in Nitrogen fixation.
| S-EPMC5339402 | biostudies-literature
Project description:MiDOG taxonomy identification validation study
| PRJNA579155 | ENA
Project description:Applying a gel-based proteomic approach, the dynamic changes in root proteins of drought treated Quercus ilex subsp. Ballota [Desf.] Samp. seedlings were followed. Water stress was applied on 20 day-old holm oak plantlets by water limitation for a period of 10 and 20 days, each followed by 10 days of recovery. Root proteins were extracted using trichloroacetate/acetone/phenol protocol and subjected to two-dimensional electrophoresis. Coomassie colloidal stained gel images were analysed and spot intensity data subjected to multivariate statistical analysis. Selected consistent spots in the three biological replicas, presenting significant changes under stress, were subjected to MALDI-TOF mass spectrometry (peptide mass fingerprinting and MS/MS). For protein identification, combined search was performed with MASCOT search engine over NCBInr Viridiplantae and Uniprot databases. Taxonomy Holm oak (Quercus ilex subsp. Ballota [Desf.] Samp.). Dentro de Q. ilex hay dos subespecies, ilex ilex e ilex Ballota.
2015-09-09 | PXD002484 | Pride
Project description:Meromictic Lake Metagenome and Taxonomy
| PRJNA489439 | ENA
Project description:Global top-down proteomics LCMS analysis of proteins purified from soybean root nodules infected with either WT or nifH- mutant Bradyrhizobium japonicum. Raw LCMS data were processed with TopPIC; combined proteoform-spectral-matches, and label free quantitation results are included as separate csv files ("*_all_PrSMs.csv", "*_LFQ_Table.csv"). Also includes MALDI-Orbitrap data of intact proteins. The MALDI raw files and xml files can be loaded into imaging software for viewing ion images. Representative summed spectra are included separately in two "IMAGE-avg11567_from100to200min.raw" files. More detailed analysis and representative proteoform ion images are discussed in the associated manuscript. For sample processing, frozen tissue were homogenized for LCMS and proteins were extracted with the MPlex protocol. For MALDI, frozen tissues were sliced and embedded on ITO slides and sprayed with DHA matrix. LCMS data were processed with TopPIC and TopPICR. Imaging data were collected with Spectroglyph software.
2022-07-26 | MSV000089984 | MassIVE
Project description:The variety of metagenomes in current databases provides a rapidly growing source of information for comparative studies. However, the quantity and quality of supplementary metadata is still lagging behind. It is therefore important to be able to identify related metagenomes by means of the available sequence data alone. We have studied efficient sequence-based methods for large-scale identification of similar metagenomes within a database retrieval context. In a broad comparison of different profiling methods we found that vector-based distance measures are well-suitable for the detection of metagenomic neighbors. Our evaluation on more than 1700 publicly available metagenomes indicates that for a query metagenome from a particular habitat on average nine out of ten nearest neighbors represent the same habitat category independent of the utilized profiling method or distance measure. While for well-defined labels a neighborhood accuracy of 100% can be achieved, in general the neighbor detection is severely affected by a natural overlap of manually annotated categories. In addition, we present results of a novel visualization method that is able to reflect the similarity of metagenomes in a 2D scatter plot. The visualization method shows a similarly high accuracy in the reduced space as compared with the high-dimensional profile space. Our study suggests that for inspection of metagenome neighborhoods the profiling methods and distance measures can be chosen to provide a convenient interpretation of results in terms of the underlying features. Furthermore, supplementary metadata of metagenome samples in the future needs to comply with readily available ontologies for fine-grained and standardized annotation. To make profile-based k-nearest-neighbor search and the 2D-visualization of the metagenome universe available to the research community, we included the proposed methods in our CoMet-Universe server for comparative metagenome analysis.
| S-EPMC4139848 | biostudies-other