Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human lung metagenome

ABSTRACT: 454 sequencing of 16S rRNA genes from endotracheal biofilms

PROVIDER: PRJNA260308 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR345301.fastq.gz	Fastqsanger.gz
	SRR345302.fastq.gz	Fastqsanger.gz
	SRR345303.fastq.gz	Fastqsanger.gz
	SRR345304.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

human tracheal metagenome

Project description:Endotracheal tube biofilms Targeted Locus (Loci)

| PRJNA295063 | ENA

human lung metagenome

Project description:Human lung microbiome 16S rRNA metagenome

| PRJNA194565 | ENA

GNPS human saliva derived in vitro biofilms

Project description:Oral in vitro biofilms were established from human saliva and grown as described in Edlund et al. 2013 (Microbiome, doi:10.1186/2049-2618-1-25). Replicate samples were collected for small molecule- and metatranscriptome analyses at pH 7 (prior to glucose amendment), pH 4.2 (6 hrs after glucose amendment) and pH 5.2 (9 hrs after glucose amendment). Other information: 16S 454-sequencing analyses exist for these communities as well as metagenomics data analyses.

2014-04-10 | MSV000078583 | GNPS

aquatic metagenome

Project description:Graywater bacteria 16S rRNA Roche 454 Sequencing

| PRJNA244266 | ENA

First exploration of the altered microbial gut-lung axis in the pathogenesis of human refractory chronic cough

Project description:v3-v4 16S rRNA sequencing was used to characterize both gut and oral microbiota composition of RCC (refractory chronic cough) patients and matched healthy controls (HC). The groups are matched in age and gender.

2024-04-17 | GSE240646 | GEO

Study of Gut Microbiome and Colorectal Tumors

Project description:Gut microbiota were assessed in 540 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples. Investigators compared gut microbiota diversity, overall composition, and normalized taxon abundance among these groups.

| 2255499 | ecrin-mdr-crc

freshwater metagenome

Project description:Freshwater Springs 16S rRNA 454 Sequences

| PRJNA195379 | ENA

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

Project description:The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the application of amplicon pyrosequencing. The possibility of barcode-tagged sequencing of templates gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing and, as in the early days of genetic community fingerprinting, pros and cons are continuously provided. In this study we investigate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of natural microbiota. Moreover, via quantitatively defined template spiking to the natural community, we explore the potential for recovering specific template ratios within complex microbial communities. For this reason, we pyrotag sequenced three biological replicates of three samples, each belonging from yearly sampling campaigns of sediment from a tar oil contaminated aquifer in Düsseldorf, Germany. Furthermore, we subjected one DNA extract to replicate technical analyses as well as to increasing ratios (0, 0.2, 2 and 20%) of 16S rRNA genes from a pure culture (Aliivibrio fisheri) originally not present in the sample. Unexpectedly, taxa abundances were highly reproducible in our hands, with max standard deviation of ~3% abundance across biological and ~2% for technical replicates. Furthermore, our workflow was also capable of recovering A. fisheri amendmend ratios in reliable amounts (0, 0.29, 3.9 and 23.8%). These results highlight that pyrotag sequencing, if done and evaluated with due caution, has the potential to robustly recapture taxa template abundances within environmental microbial communities. 9 Biological and 3 technical replicates were evaluated, as well as potential to recover qPCR-defined ratios of DNA, in 454 pyrotag sequencing

2012-07-16 | E-GEOD-35631 | biostudies-arrayexpress

human metagenome

Project description:Human Microbiome Project (HMP) 16S rRNA Gene Diversity, the diversity of 16S ribosomal RNA genes in the human microbiome: 454 Protocol Validation - Clinical

| PRJNA48339 | ENA

human metagenome

Project description:Human Microbiome Project (HMP) 16S rRNA Gene Diversity, the diversity of 16S ribosomal RNA genes in the human microbiome: 454 Protocol Development - Clinical

| PRJNA48467 | ENA

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