Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Subsurface geothermal aquifer 16S metabarcoding

ABSTRACT: subsurface geothermal aquifer 16S metabarcoding

PROVIDER: PRJEB41672 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR9765680_1.fastq.gz	Fastqsanger.gz
	ERR9765680_2.fastq.gz	Fastqsanger.gz
	ERR9765690_1.fastq.gz	Fastqsanger.gz
	ERR9765690_2.fastq.gz	Fastqsanger.gz
	ERR9765700_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 58

Similar Datasets

subsurface geothermal aquifer MAGs

Project description:subsurface geothermal aquifer MAGs

| PRJEB51955 | ENA

Subsurface geothermal aquifer MAGs

Project description:Subsurface geothermal aquifer MAGs

| PRJEB56575 | ENA

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). 15 samples examined in total from important plume zones of the aquifer sampled in Feb. 2006, Sep. 2008 and Jun. 2009 (5 every year of sampling).

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

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

2012-11-11 | GSE25345 | GEO

subsurface metagenome

Project description:Geothermal fumarole subsurface microbial communities from Mt. Erebus, Antarctica

| PRJNA431961 | ENA

Metabarcoding (16S rRNA) from Concepcion bay, Chile

Project description:Metabarcoding (16S rRNA) from Concepcion bay, Chile

| PRJEB57258 | ENA

aquifer metagenome

Project description:Metagenome from a deep subsurface, shale-hosted aquifer of the Volcanic Eifel

| PRJNA627655 | ENA

Selective phylogenetic analysis targeted at 16S rRNA genes of thermophiles and hyperthermophiles in deep-subsurface geothermal environments.

Project description:Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76 degrees C) and river water (14 degrees C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82 degrees C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84 degrees C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84 degrees C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained.

| S-EPMC1352187 | biostudies-literature

Brassica napus soil metabarcoding ADNr 16S & ITS1

Project description:Brassica napus soil metabarcoding ADNr 16S & ITS1 Raw sequence reads

| PRJNA854370 | ENA

Expression analysis in anaerobic Hanford 100H aquifer flow-through columns receiving lactate and chromate

Project description:Columns containing Hanford 100H aquifer sediment continuously infused with 5 mM lactate, 5 uM Cr(VI), and either 7.5 mM sulfate or 12 mM nitrate as an electron acceptor.

2014-04-08 | GSE56554 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data