Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic RNA-sequencing analysis of the hypervirulent Clostridioides difficile R20291 strain in response to trehalose

ABSTRACT: Transcriptomic RNA-sequencing analysis of the hypervirulent Clostridioides difficile R20291 strain in response to trehalose

PROVIDER: PRJNA970676 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24477505_1.fastq.gz	Fastqsanger.gz
	SRR24477505_2.fastq.gz	Fastqsanger.gz
	SRR24477506_1.fastq.gz	Fastqsanger.gz
	SRR24477506_2.fastq.gz	Fastqsanger.gz
	SRR24477507_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Transcriptomic RNA-sequencing analysis of the hypervirulent Clostridioides difficile R20291 strain in response to trehalose

Project description:Clostridioides difficile, the leading cause of antibiotic-associated diarrhoea worldwide, is a genetically diverse species which can metabolise a number of nutrient sources upon colonising a dysbiotic gut environment. Trehalose, a disaccharide sugar consisting of two glucose molecules bonded by an α 1,1-glycosidic bond, has been hypothesised to be involved in the emergence of C. difficile hypervirulence due to its increased utilisation by the RT027 and RT078 strains. Using RNA-sequencing analysis, we report the identification of a putative trehalose metabolism pathway which is induced during growth in trehalose: this has not been previously described within the C. difficile species. These data demonstrate the metabolic diversity exhibited by C. difficile which warrants further investigation to elucidate the molecular basis of trehalose metabolism within this important gut pathogen.

2023-05-26 | GSE232033 | GEO

Clostridioides difficile: R20291_pMTL84151 transconjugant (C) vs. R20291_pMTL84151-03890 (T1)

Project description:Gene expression level of Clostridioides difficile (C. difficile) strain R20291 comparing control C. difficile carring pMTL84151 as vector plasmid with C. difficile conjugated with a pMTL84151-03890 gene. Goal was to determine the effects of 03890 gene conjugation on C. difficile strain R20291 gene expression.

2023-11-30 | GSE219066 | GEO

Transcriptomic profile of a Clostridioides difficile rsbW deletion mutant compared to parental R20291 strain

Project description:RNA-seq was conducted to uncover the regulatory roles of RsbW in the lifestyle of Clostridioides difficile strain R20291. RNA were extracted from planktonic cultures, which were grown in BHI-S (Sigma-Aldrich, USA) to early stationary phase (10h). The cells were re-suspended in LETS buffer and lysed using Fast-prep 24 instrument (MP Bioscience) and RNA was extracted using 1 ml Trizol (Ambion, USA). Samples were cleaned and sequenced by Novogene Company Limited, PE150 with approximately 10 million reads per sample. After QC, reads were aligned to R20291 (NC_013316.1) with Bowtie2 and readcounts were generated with Samtools and Bedtools. Differential gene expression analysis was conducted with DESeq2 with a p-value of 0.05, differential gene expression was determined with ± -2 logFC.

2022-08-22 | E-MTAB-12114 | biostudies-arrayexpress

Clostridioides difficile R20291

Project description:Clostridioides difficile R20291 Transcriptome or Gene expression

| PRJNA283975 | ENA

Clostridioides difficile R20291

Project description:Clostridioides difficile R20291 Genome sequencing and assembly

| PRJNA471285 | ENA

Clostridioides difficile R20291

Project description:Clostridioides difficile R20291 Transcriptome or Gene expression

| PRJNA416052 | ENA

Clostridioides difficile R20291

Project description:Clostridium difficile R20291 genome sequencing project

| PRJNA38039 | ENA

Clostridium difficile transcriptome of strain R20291 in response to cysteine by using a time-resolved RNA-seqencing

Project description:The incidence of Clostridium difficile infection has been steadily rising over the past decade. Its increased rate is associated with the specific NAP1/BI/027 strains which are “hypervirulent” and have led to several large outbreaks since their emergence. However, the relation between their outbreaks and virulence regulation mechanisms remains unclear. It has been reported that the major virulence factor TcdA and TcdB in C. difficile could be repressed by cysteine. Here, we investigated functional and virulence-associated regulation of C. difficile R20291 in response to cysteine stress by using a time-resolved genome-wide transcriptional analysis. Dramatic changes of gene expression in C. difficile were revealed in functional categories related to transport, metabolism, and regulators under cysteine stress during different phases of growth.

2020-12-12 | GSE107961 | GEO

Clostridioides difficile R20291

Project description:Clostridioides difficile CRISPR-cas9 system

| PRJNA398796 | ENA

Differential stress transcriptome landscape of historic and recently emerged hypervirulent strains of Clostridium difficile strains determined using RNA-seq

Project description:Purpose: To determine how divergent strains of C. difficile respond to environmental changes, the transcriptomes of two historic and two recently isolated hypervirulent strains were analyzed following nutrient shift and osmotic shock. Methods: Following nutrient shift and osmotic shock, mRNA profile were determined using sequing of transcriptome in biological duplicates, using Illumina Hi-seq 2000. Results: After applying the quality control steps, for each sample, sequence reads were 90 nucleotides in length and the total number of reads per sample was ~ 26.6 million on average. Expression of more than 90% CDS was detected under the three experimental conditions combined. About 20% of these genes were indentified to be differentially expressed at 1.5 fold or more. Conclusions: Our results reveal that although C. difficile strains contain a large number of shared and strain specific genes, the majority of the differentially expressed genes were core genes. We also detected a number of transcriptionally active regions that were not part of the primary genome annotation. Some of these are likely to be small regulatory RNAs. Differential stress transcriptomes of two historic (strain 630 and 196) and two recently emerged hypervirulent strains (stain R20291 and 32g58) of C. difficile was determined by deep sequencing, in duplicate, using Illumina Hi-Seq 2000.

2013-11-06 | E-GEOD-50497 | biostudies-arrayexpress

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