Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prokaryotic metagenome

ABSTRACT: prokaryotic metagenome Metagenome

PROVIDER: PRJNA608846 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11671800_1.fastq.gz	Fastqsanger.gz
	SRR11671800_2.fastq.gz	Fastqsanger.gz
	SRR11671801_1.fastq.gz	Fastqsanger.gz
	SRR11671801_2.fastq.gz	Fastqsanger.gz
	SRR11671789_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 26

Similar Datasets

prokaryotic bacterium metagenome

Project description:prokaryotic bacterium metagenome Raw sequence reads

| PRJNA1221977 | ENA

Soil metagenome from avocado orchards in Channybearup, Western Australia in 2024

Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.

2025-06-15 | GSE298403 | GEO

An optimized RNA amplification method for prokaryotic expression profiling analysis

2009-07-25 | GSE17074 | GEO

Prokaryotic Proteogenomics

Project description:Prokaryotic Proteogenomics

| PRJNA66995 | ENA

Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

Project description:We present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a high-throughput prokaryotic scRNA-seq pipeline. We demonstrated that PETRI-seq effectively barcoded single bacterial cells in a species-mixing experiment with E. coli (MG1655) and S. aureus (USA300). Within the S. aureus population, we found rare prophage induction in 0.04% of cells. We further demonstrated that PETRI-seq was able to distinguish between E. coli growth phases based on mRNA expression patterns by combining stationary E. coli with exponential E. coli in multiple experiments.

2020-05-25 | GSE141018 | GEO

An optimized RNA amplification method for prokaryotic expression profiling analysis

Project description:Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model. To identify an optimal RNA labeling method for prokaryotic microarray analysis, experiments were performed with starting RNA obtained from E.coli growing at control (37Â°C) or heat shock (43Â°C) condition. We employed 0.5 Î¼g of total RNA for a single round of amplification using PAOD and RPA methods coupling to IVT to generate cDNA targets. In addition, an approach using DL method was also performed. Three types of cDNA mixtures containing Cy5-labeled (or Cy3-labeled) control DNA and Cy3-labeled (or Cy5-labeled) DNA targets were hybridized with E.coli microarrays in a dye-swap strategy. Replicate experiments were conducted from the same batch of total RNA to assess technique reproducibility of each approach.

2010-05-15 | E-GEOD-17074 | biostudies-arrayexpress

Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast

Project description:A biosensor, consisting of the prokaryotic cis,cis-muconic acid-binding transcriptional activator BenM and an engineered reporter was successfully transplanted into bakers yeast Saccharomyces cerevisiae. RNAseq data used to assess the transcription orthogonality of BenM in yeast cells is presented here.

2016-08-01 | E-MTAB-4836 | biostudies-arrayexpress

Gene Expression in Prokaryotic Microbial Assemblages Across Salinity Gradients in the Columbia River Coastal Margin

Project description:Analysis of microbial gene expression in response to physical and chemical gradients forming in the Columbia River, estuary, plume and coastal ocean was done in the context of the environmental data base. Gene expression was analyzed for 2,234 individual genes that were selected from fully sequenced genomes of 246 prokaryotic species (bacteria and archaea) as related to the nitrogen metabolism and carbon fixation. Seasonal molecular portraits of differential gene expression in prokaryotic communities during river-to-ocean transition were created using freshwater baseline samples (268, 270, 347, 002, 006, 207, 212).

2010-09-10 | GSE18303 | GEO

Prokaryotic N1-methyladenosine erasers maintain tRNA m1A modification levels in Streptomyces venezuelae.

Project description:tRNA modifications help maintain tRNA structure and facilitate stress responses. Found in all three kingdoms of life, m1A tRNA modification occurs in the T loop of many tRNAs and stabilizes tertiary tRNA structure and impacts translation. M1A in T loop is known to be reversible by three mammalian demethylase enzymes, which bypasses the need of turning over the tRNA molecule to adjust their m1A levels in cells. However, no prokaryotic tRNA demethylase enzyme has been identified. Using Streptomyces venezuelae as a model organism, we confirmed the presence and quantitative m1A tRNA signatures using mass spectrometry and high throughput tRNA sequencing. We identified two RNA demethylases that can remove m1A in tRNA and confirmed the activity of a previously annotated tRNA m1A writer. Using single gene knockouts of these erasers and the m1A writer, we subjected these strains to stress conditions and found dynamic changes to m1A levels in many tRNAs. Phenotypic characterization highlighted changes to their growth and altered antibiotic production. Our identification of the first prokaryotic tRNA demethylase enzyme paves the way for investigating new mechanisms in global translational regulation in bacteria.

2024-06-20 | GSE264330 | GEO

Metagenome sequencing of prokaryotic microbiota collected from Byron Glacier, Alaska.

Project description:Cold environments, such as glaciers, are large reservoirs of microbial life. The present study employed 16S rRNA gene amplicon metagenomic sequencing to survey the prokaryotic microbiota on Alaskan glacial ice, revealing a rich and diverse microbial community of some 2,500 species of bacteria and archaea.

| S-EPMC3623000 | biostudies-literature

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