Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

5’-NAD-RNA identification in E. coli BW25113 wt, nudC and csdA knockouts

ABSTRACT: 5’-NAD-RNA identification in E. coli BW25113 wt, nudC and csdA knockouts

PROVIDER: PRJNA934575 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23348254_1.fastq.gz	Fastqsanger.gz
	SRR23348254_2.fastq.gz	Fastqsanger.gz
	SRR23348255_1.fastq.gz	Fastqsanger.gz
	SRR23348255_2.fastq.gz	Fastqsanger.gz
	SRR23348256_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

5’-NAD-RNA identification in E. coli BW25113 wt, nudC and csdA knockouts

Project description:In the present study we applied NAD captureSeq to charecterize the 5'-NAD-RNA profile of E. coli BW25113 wt strain as well as nudC and csdA knockouts. The data obtained showed that both knockouts resulted in an increased number of identified 5’-NAD-RNA species, thus suggesting that CsdA might add a potentially new layer of control on NAD-epitranscriptomic landscape.

2023-08-22 | GSE224605 | GEO

Whole transcriptome sequencing of E. coli BW25113 wt and nudC knockout strains

Project description:In the present study we performed total RNA sequencing of E. coli BW25113 wt and nudC knockout strains. RNA-seq analysis revealed that the inactivation of nudC gene in bacteria shows alteration of level of sRNA and protein-coding transcripts mainly associated with bacterial chemotaxis and flagellar assembly pathways.

2023-08-22 | GSE224606 | GEO

Identification of NAD+ capped mRNAs in S. cerevisiae

Project description:We report the identification of NAD-RNA in the yeast Saccharomyces cerevisiae under two distinct growth mediums.

2016-11-30 | GSE90636 | GEO

Assessing the effects of transcription factor knockouts on growth in high-density fed-batch cultures

Project description:We used RNA-seq to investigate the effects of single transcription factor knockouts on growth of E. coli BW25113 in fed-batch cultures at multiple timepoints. Cells were grown in an ambr automated bioreactor and maintained at 30 degrees and pH 6.5 in Medium C.

2022-12-30 | GSE221706 | GEO

NAD tagSeq, a new method for transcriptome-wide identification and quantification of NAD+-capped RNAs, revealed that NAD+-capped RNAs are produced from a large number of protein-coding genes in Arabidopsis

Project description:The 5’ end of a eukaryotic mRNA generally has a methyl guanosine cap (m7G cap) that not only protects the mRNA from degradation but also mediates almost all other aspects of gene expression. Some RNAs in E. coli, yeast, and mammals were recently found to contain an NAD+ cap at their 5’ ends. Here we report development of a new method – NAD tagSeq – for transcriptome-wide identification and quantification of NAD+-capped RNAs (NAD-RNAs). The method uses first an enzymatic reaction and then a click chemistry reaction to label NAD-RNAs with a synthetic RNA tag. The tagged RNA molecules can be enriched and directly sequenced using the Oxford Nanopore sequencing technology. NAD tagSeq not only allows more accurate identification and quantification of NAD-RNAs but can also reveal sequences of whole NAD-RNA transcripts. Using NAD tagSeq, we found that NAD-RNAs in Arabidopsis are mostly produced from a few thousand protein-coding genes, with over 60% of them from fewer than 200 genes. The top 2,000 genes that were found to produce the highest numbers of NAD-RNAs were enriched in the gene ontology terms of responses to oxidative stress and other stresses, photosynthesis, and protein synthesis. For some Arabidopsis genes, over 10% of their transcripts could be NAD-capped. The NAD-RNAs in Arabidopsis have similar overall sequence structures to their canonical m7G-capped mRNAs. The identification and quantification of NAD-RNAs and revealing their sequence features provide essential steps toward understanding functions of NAD-RNAs.

2019-07-01 | GSE127755 | GEO

BW25113 Rif pre-treated persister cells vs. stationary phase BW25113 wild-type

Project description:E. coli K-12 BW25113 persister cells generated via rifampicin pre-treatment relative to BW25113 wild-type stationary phase gene expression. Persister cells were generated following exposure to ampicillin 20 ug/mL.

2016-11-20 | GSE34177 | GEO

BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type

Project description:E. coli K-12 BW25113 persister cells generated via H202 pre-treatment and deletion of rpoS, relative to BW25113 wild-type stationary phase gene expression. Persister cells were generated following exposure to ampicillin 20 ug/mL.

2012-04-03 | GSE34028 | GEO

E. coli BW25113 ompA mutant vs wild type biofilm and E. coli BW25113 ompA/pCA24N_ompA vs ompA/pCA24N suspension cells

Project description:This Series involves two studies: 1) The gene expression of E. coli K-12 BW25113 ompA mutant strain vs. wild type strain glasswool biofilm cells and E. coli K-12 BW25113 ompA mutant vs. wild type polystyrene biofilm cells. 2) The gene expression of E. coli BW25113 ompA/pCA24N_ompA vs. ompA/pCA24N suspension cells.

2010-01-20 | GSE14064 | GEO

E. coli K12 Bw25113/pCA24N-hha with 2 mM IPTG vs BW25113/pCA24N with 2 mM IPTG

Project description:gene expression profiles by overexpressing Hha from pCA24N-hha using 2 mM IPTG induction in BW25113 wild type suspension cells in LB medium at 37C relative to BW25113 carrying the empty vector plasmid in the same test conditions. Keywords: overexpression, gene expression profiles

2008-06-17 | GSE10116 | GEO

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD+-capped transcripts

Project description:We developed a Copper-free, strain-promoted azide-alkyne cycloaddition reaction (SPAAC) to capture NAD-RNAs without RNA degradation. We examined the specificity of CuAAC and SPAAC reactions towards NAD+ vs. m7G, and found that both prefer NAD+ but also act on m7G. We show that m7G-capped RNA can be immuno-depleted, allowing for the specific identification of NAD-RNA via the SPAAC reaction and sequencing, which we name SPAAC-NAD-seq. Subjecting Arabidopsis RNA to both the original NAD captureSeq and SPAAC-NAD-seq, we found that more NAD+-capped RNA was identified by the latter, particularly those with low abundance. This led to the discovery of new gene ontology terms such as starch biosynthsis, intracellular protein transport and response to cadmium stress associated with genes that produce NAD-RNA. Furthermore, reads were uniformly distributed along gene bodies, which suggested that SPAAC-NAD-seq retained full-length sequence information. SPAAC-NAD-seq enables specific and efficient discovery of NAD-RNA in prokaryotes, and when combined with m7G-RNA depletion, in eukaryotes.

2021-04-14 | GSE162114 | 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