Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Aquatic metagenome

ABSTRACT: Bacterial 16S amplicon 454 pyrosequencing of environmental samples (vertebrate faeces, sediment, soil, surface water) to assess the potential of next generation sequencing methods for health related microbial water quality monitoring

PROVIDER: PRJNA276049 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1813130.fastq.gz	Fastqsanger.gz
	SRR1813190.fastq.gz	Fastqsanger.gz
	SRR1813071.fastq.gz	Fastqsanger.gz
	SRR1813101.fastq.gz	Fastqsanger.gz
	SRR1813131.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 38

Similar Datasets

High-throughput transcriptomics of water extracts detects reductions in biological activity with water treatment processes

Project description:The presence of numerous chemical contaminants from industrial, agricultural, and pharmaceutical sources in water supplies poses a potential risk to human and ecological health. Current chemical analyses suffer from limitations including chemical coverage and high cost, and broad-coverage in vitro assays such as transcriptomics may further improve water quality monitoring by assessing a large range of possible effects. Here, we used high-throughput transcriptomics to assess the activity induced by field-derived water extracts in MCF7 breast carcinoma cells.

2024-03-05 | GSE252117 | GEO

High-throughput 16S rRNA amplicon pyrosequencing of contaminated aquifer sediment

Project description:Contaminated aquifer (Dusseldorf-Flinger, Germany) templates extracted from 5 sediment depths ranging between 6.4 and 8.4 m below ground and over 3 years of sampling were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads were furhter trimmed for quality and lenght (>250 bp).

2012-11-11 | GSE25345 | GEO

High-throughput sequencing of small RNAs from Arabidopsis thaliana

Project description:High-throughput sequencing of Arabidopsis thaliana endogenous small RNAs by 454 pyrosequencing. Keywords: high-throughput sequencing

2006-11-02 | GSE5228 | GEO

aquatic metagenome

Project description:Amplicon-based pyrosequencing of protistan parasites in ships' ballast water

| PRJNA294684 | ENA

High-throughput 16S rRNA amplicon pyrosequencing of contaminated aquifer sediment

2012-11-11 | E-GEOD-25345 | biostudies-arrayexpress

Aquatic decomposition and its effects on the bone proteome for forensic applications

Project description:Methods currently available to estimate the post-mortem submerged interval (PMSI) of cadavers in water suffer from poor accuracy, being mostly based on morphological examination of the remains. Proteins present within bones have recently attracted more attention from researchers interested in the estimation of the post-mortem interval (PMI) in terrestrial environments. Despite the great potential of proteomic methods for PMI estimation, their application to aquatic environments has not yet been explored. In this study, we examined whether four different types of aquatic environment (tap water, saltwater, pond water and chlorinated water) affected the proteome of mice bones with increasing PMSIs (from zero to three weeks).

2020-04-06 | PXD017386 | Pride

siRNAs 15-29 nucleotides long with 100 percent hit to Turnip mosaic virus clone GBR98

Project description:Mustard (Brassica juncea) was tested for Turnip mosaic virus infection. Small RNA of the plant was extracted and converted to DNA according to Ho, T., et al. (2006) Journal of Virological Methods 136:217-223, with primers modified to contain 454 adapter nucleotide sequences. The DNA then passed quality control through Bioanalyzer and Nanodrop before sequenced by 454 Life Sciences. Keywords: siRNA

2008-09-12 | GSE12053 | GEO

RNA-seq transcriptomic profiling for self-renewing (SR) and senescent (SEN) human adult adipose derived mesenchymal stem cells (hADSCs)

Project description:Characterization of gene expression levels with RNA-seq was performed on self-renewing (SR) and senescent (SEN) human adult adipose derived mesenchymal stem cells (hADSCs) using the Roche 454 pyrosequencing platform.

2017-08-15 | GSE77284 | GEO

Small RNAs from the lycopod Selaginella moellendorffii

Project description:The small RNAs of Selaginella moellendorffii were sampled by direct pyrosequencing (454 Life Sciences). These data represent microRNAs, siRNAs, and other expressed small RNAs of ~18-~28 nts. in length. Keywords: Small RNA sequencing - high throughput

2007-06-30 | GSE7320 | GEO

siRNAs 15-29 nucleotides long with 100 percent hit to Turnip mosaic virus clone GBR98

2008-09-11 | E-GEOD-12053 | biostudies-arrayexpress