Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Marine sediment metagenome

ABSTRACT: Aarhus Bay sediment PCR amplified product sequencing

PROVIDER: PRJNA208115 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR924161.fastq.gz	Fastqsanger.gz
	SRR924162.fastq.gz	Fastqsanger.gz
	SRR924163.fastq.gz	Fastqsanger.gz
	SRR924164.fastq.gz	Fastqsanger.gz
	SRR924165.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

marine sediment metagenome

Project description:Aarhus Bay M5 station metagenome and metatranscriptome sequencing 0-35 cmbs sediment Genome sequencing and assembly

| PRJNA1021937 | ENA

marine sediment metagenome

Project description:Diversity of archaeal and bacterial 16S rRNA gene in marine sediment in Aarhus Bay

| PRJNA387358 | ENA

Bay Station M5 sediment metagenome sequencing

Project description:Aarhus Bay Station M5 sediment metagenome sequencing

| PRJNA454851 | 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).

2012-11-11 | GSE25345 | GEO

marine sediment metagenome

Project description:Amplicon sequencing of phytoplankton assemblages in sediment cores in Onagawa Bay

| PRJDB8175 | ENA

sediment metagenome

Project description:Long- and short-read metagenome assembly from Aarhus Bay sediments

| PRJNA596167 | ENA

marine sediment metagenome

Project description:Nitrogen-cycling microbial communities in San Francisco Bay sediment

| PRJNA285824 | ENA

marine sediment metagenome

Project description:Marine Sediment from the Berkeley Bay Targeted Locus (Loci)

| PRJNA266453 | ENA

Identification of Arsenic Resistance Genes from Marine Sediment Metagenome.

Project description:A metagenomic library of sea sediment metagenome containing 245,000 recombinant clones representing ~ 2.45 Gb of sea sediment microbial DNA was constructed. Two unique arsenic resistance clones, A7 and A12, were identified by selection on sodium arsenite containing medium. Clone A7 showed a six-fold higher resistance to arsenate [As(V)], a three-fold higher resistance to arsenite [As(III)] and significantly increased resistance to antimony [Sb(III)], while clone A12 showed increased resistance only to sodium arsenite and not to the other two metalloids. The clones harbored inserts of 8.848 Kb and 6.771 Kb, respectively. Both the clones possess A + T rich nucleotide sequence with similarity to sequences from marine psychrophilic bacteria. Sequence and transposon-mutagenesis based analysis revealed the presence of a putative arsenate reductase (ArsC), a putative arsenite efflux pump (ArsB/ACR) and a putative NADPH-dependent FMN reductase (ArsH) in both the clones and also a putative transcriptional regulatory protein (ArsR) in pA7. The increased resistance of clone A7 to As(V), As(III) and Sb(III) indicates functional expression of ArsC and ArsB proteins from pA7. The absence of increased As(V) resistance in clone A12 may be due to the expression of a possible inactive ArsC, as conserved Arg60 residue in this protein was replaced by Glu60, while the absence of Sb(III) resistance may be due to the presence of an ACR3p-type arsenite pump, which is known to lack antimony transport ability.

| S-EPMC5574776 | biostudies-literature

sediment metagenome

Project description:Marine (Aarhus) and freshwater (Lake Constance) sediment Raw sequence reads

| PRJNA393823 | ENA