Ontology highlight
ABSTRACT:
PROVIDER: PRJNA186588 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis. Using SARST-V6, we obtained bacterial profiles for each drinking water sample, demonstrating a strikingly high degree of biodiversity dominated by a large collection of low-abundance phylotypes. In all water samples, between 57.2-77.4% of the sequences obtained indicated bacteria belonging to the Proteobacteria phylum. Full-length 16S rDNA sequences were also generated for each sample, and comparison of the RSTs with these sequences confirmed the accurate assignment for several abundant bacterial phyla identified by SARST-V6 analysis, including members of unclassified bacteria, which account for 6.3-36.5% of all V6 sequences. These results suggest that these bacteria may correspond to a common group adapted to drinking water systems. The V6 primers used were subsequently evaluated with a computer algorithm to assess their hybridization efficiency. Potential errors associated with primer-template mismatches and their impacts on taxonomic group detection were investigated. The biodiversity present in all three drinking water samples suggests that the bacterial load of the drinking water leaving treatment plants may play an important role in determining the downstream community dynamics of water distribution networks. 3 different drinking water samples (Orly, Ivry, Joinville drinking water sample)
2009-01-07 | E-GEOD-14318 | biostudies-arrayexpress
Project description:We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis. Using SARST-V6, we obtained bacterial profiles for each drinking water sample, demonstrating a strikingly high degree of biodiversity dominated by a large collection of low-abundance phylotypes. In all water samples, between 57.2-77.4% of the sequences obtained indicated bacteria belonging to the Proteobacteria phylum. Full-length 16S rDNA sequences were also generated for each sample, and comparison of the RSTs with these sequences confirmed the accurate assignment for several abundant bacterial phyla identified by SARST-V6 analysis, including members of unclassified bacteria, which account for 6.3-36.5% of all V6 sequences. These results suggest that these bacteria may correspond to a common group adapted to drinking water systems. The V6 primers used were subsequently evaluated with a computer algorithm to assess their hybridization efficiency. Potential errors associated with primer-template mismatches and their impacts on taxonomic group detection were investigated. The biodiversity present in all three drinking water samples suggests that the bacterial load of the drinking water leaving treatment plants may play an important role in determining the downstream community dynamics of water distribution networks.
2009-01-08 | GSE14318 | GEO
Project description:We investigate the functional complexity of the Plutella xylostella transcriptome in defending against a Bt toxin using Illumina sequencing technology. Over 2,900 differentially expressed unigenes were obtained in resistant P. xylostella comparison to their susceptible counterpart. All the P. xylostella were maintained on cabbage.The susceptible strain (MM) was cultured without exposure to any Bt toxins.Before the sample collected, Cry1Ac-resistant P. xylostella were treated with 750μg/mL Bt toxin Cry1Ac to eliminate the heterozygous individuals. Then the survivors were collected after 48 hours and designed as the resistant sample (MK and GK). Then fourth-instars larvae midgut tissues of MK,GK and MM were collected, respectively, The RNA was extracted and sequenced using Illunima HiSeq 2000.
2014-05-01 | E-GEOD-46399 | biostudies-arrayexpress
Project description:We investigate the functional complexity of the Plutella xylostella transcriptome in defending against a Bt toxin using Illumina sequencing technology. Over 2,900 differentially expressed unigenes were obtained in resistant P. xylostella comparison to their susceptible counterpart.
2014-05-01 | GSE46399 | GEO
Project description:Hypervariable regions V3-V5 of bacterial 16S rRNA genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-03-14 | E-ERAD-254 | biostudies-arrayexpress
Project description:Plutella xylostella is the major cosmopolitan pest of brassica and other crucifer crops,the larval midgut of which is a dynamic organ that interfaces with a diversearray of physiological and toxicological processes.The draft sequence of the P.xylostella genome was recently released,but its annotation remains chanllenging because of the low coverage of this branch of life.Peptide sequencing by computational assignment of tandem mass spectra to a database of putative protein sequences provides an independent approach to confirm or refute protein prediction,which has been termed proteogenomics.In this study,we carried out an in-depth proteogenomic analysis using shotgun HPLC-ESI-MS/MS approach with a multi-algorithme peipline to complement genome annotation in the P.xylostella larval midgut.
2016-04-11 | PXD003567 | Pride