Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Insights into Simultaneous Microbial Chromium and Nitrate Reduction at Different pH: Performance comparison and differential expression

PROVIDER: PRJNA561680 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10015225_1.fastq.gz	Fastqsanger.gz
	SRR10015225_2.fastq.gz	Fastqsanger.gz
	SRR10015226_1.fastq.gz	Fastqsanger.gz
	SRR10015226_2.fastq.gz	Fastqsanger.gz
	SRR10015227_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

time course uranyl nitrate response-Transcriptomic analysis of uranyl response in Arabidopsis thaliana

Project description:cea06-01_uranyl_nitrate - time course uranyl nitrate response - Dynamic analyses of transcriptomic response to urany l nitrate - Plants are grown on sand and transfert in hydroponic culture during 2 days and then expose or not to 50uM uranyl nitrate at pH 4.5 in water or only to water at pH 4.5. Roots and leaves were collected independently after 2h, 6h and 30h of treament. Keywords: organ comparison,time course,treated vs untreated comparison

2008-06-17 | GSE11797 | GEO

Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues

Project description:Single-cell transcriptomics has emerged as the preferred tool to define cell identity through the analysis of gene expression signatures. However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of three well-established high throughput 3’-scRNAseq platforms: Drop-seq, 10x Chromium and BD Rhapsody; using tumours that present high cell diversity. Our experimental design includes both fresh and artificially damaged samples from the same tumours, which also provides a comparable dataset to examine their performance under challenging conditions. The performance metrics used in this study consist of gene sensitivity, mitochondrial content, reproducibility, clustering capabilities, cell type representation and ambient RNA contamination. These analyses showed that BD Rhapsody and 10x Chromium have similar but higher gene sensitivity than Drop-seq, while BD Rhapsody has the highest mitochondrial content. Interestingly, we found cell type detection biases between platforms, including a lower proportion of endothelial and myofibroblast cells in BD Rhapsody and lower gene sensitivity in granulocytes for 10x Chromium. Moreover, the source of the ambient noise was different between plate-based and droplet-based platforms. In conclusion, our reported platform differential performance should be considered for the selection of the scRNAseq method during the study experimental designs.

2024-09-04 | GSE229765 | GEO

sludge metagenome

Project description:Metagenomic data of microbially mediated stimultaneous chromate and nitrate reduction at different pH

| PRJNA574797 | ENA

time course uranyl nitrate response-Transcriptomic analysis of uranyl response in Arabidopsis thaliana

2010-05-26 | E-GEOD-11797 | biostudies-arrayexpress

Project description:Nitrate dissimilatory reduction

| PRJNA950209 | ENA

Project description:Enhancement effect of minerals on microbial simultaneous nitrate and Cr(VI) reduction

| PRJNA642007 | ENA

atnar2.1-1-Atnar2.1-1 response to transfer on low nitrate condition

Project description:ra05-12_nar2 - atnar2.1-1 - Does the ko of AtNAR2.1 leads to a differential expression in comparison to the WT when grown under high nitrate condition and transfered onto low nitrate concentration? - Plants were grown for 41 days in hydroponics in media containing 6 mM nitrate and then transferred to 6 or 0.2 mM nitrate media for 24h ( short days, irradiation 150 uE). Plants were harvested on day 42 during the first 2 hours of light. Keywords: dose response,gene knock out

2008-03-12 | GSE10705 | GEO

Transcriptome analysis of the shoots of Arabidopsis wild-type and mutants deficient in either or both activities of nitrate reductase and alternative oxidase

Project description:The conversion of nitrate to ammonium, known as nitrate reduction, consumes large amounts of reductants in plants. Previous studies have observed that mitochondrial alternative oxidase (AOX) is upregulated under conditions of limited nitrate reduction, such as low or no nitrate availability, or when ammonium serves as the sole nitrogen (N) source. Electron transfer from ubiquinone to AOX bypasses the proton-pumping complexes III and IV, thereby consuming reductants efficiently. Therefore, the upregulation of AOX under conditions of limited nitrate reduction may help dissipate excessive reductants and mitigate oxidative stress. However, firm evidence supporting this hypothesis is lacking due to the absence of experimental systems capable of directly analyzing the relationship between nitrate reduction and AOX. To address this gap, we developed a novel culturing system that allows for the manipulation of nitrate reduction and AOX activities separately, without inducing N starvation, ammonium toxicity, or disrupting the nitrate signal. Using this system, we investigated genome-wide gene expression with RNA-seq to gain insight into the relationship between AOX and nitrate reduction.

2024-04-23 | E-MTAB-14027 | biostudies-arrayexpress

Proteomic response of Alicycliphilus denitrificans strain BC towards the different electron acceptors chlorate, nitrate and oxygen.

Project description:Alicycliphilus denitrificans is a versatile, ubiquitous, facultative anaerobic bacterium. A. denitrificans strain BC can use chlorate, nitrate and oxygen as electron acceptor for growth. Cells display a prolonged lag-phase when transferred from nitrate to chlorate and vice versa. Furthermore, cells adapted to aerobic growth do not easily use nitrate or chlorate as electron acceptor. We further investigated these responses of strain BC by differential proteomics, transcript analysis and enzyme activity assays. In nitrate-adapted cells transferred to chlorate and vice versa, appropriate electron acceptor reduction pathways need to be activated. In oxygen-adapted cells, adaptation to the use of chlorate or nitrate is likely difficult due to the poorly active nitrate reduction pathway and low active chlorate reduction pathway. We deduce that the Nar-type nitrate reductase of strain BC also reduces chlorate, which may result in toxic levels of chlorite if cells are transferred to chlorate. Furthermore, the activities of nitrate reductase and nitrite reductase appear to be not balanced when oxygen-adapted cells a shifted to nitrate as electron acceptor, leading to the production of a toxic amount of nitrite. These data suggest that strain BC encounters metabolic challenges in environments with fluctuations in the availability of electron acceptors. Proteomic samples were prepared from Alicycliphilus denitrificans grown in the presence of different electron acceptors: chlorate, nitrate and oxygen. Proteins were separated by a short SDS gel and for each sample 4 in-gel digest slices were prepared. Peptide samples were measured by nLC LTQ-Orbitrap and the data were analysed with MaxQuant using default settings (1% FDR on peptide and protein level) and filtered extra to keep only proteins identified with at least 2 peptides and 1 unique and 1 unmodified peptide.

2013-08-12 | PXD000258 | Pride

Does Dietary Nitrate Supplementation Improve Aerobic Performance

Project description:The purpose of this study is to determine whether dietary nitrate supplementation improves performance in cardiopulmonary exercise testing (CPET).

| 2180461 | ecrin-mdr-crc

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