Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of Salmonella enterica Typhimurium LT2

ABSTRACT: We performed whole-genome transcriptomic analyses of the Salmonella Typhimimurium genome during glucose-phosphate stress. In particular, we wanted to elucidate the role of the the small RNA SgrS and protein regulator SgrT in the stress response. Wild-type Salmonella cells, mutants of Salmonella either lacking sgrS or lacking SgrS RNA/ SgrT peptide function were subject to glucose-phoshate stress

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

SUBMITTER: Brian Tjaden

PROVIDER: E-GEOD-45445 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA. Illumina RNA-Seq of total RNA extracted from wild-type, SgrR/SgrS mutant and SgrS overexpressing E. coli strains grown in different conditions.

2013-03-26 | E-GEOD-45443 | biostudies-arrayexpress

RNAseq analysis of the serotype M1 group A Streptococcus strain MGAS2221

Project description:We recovered RNA from exponential and stationary phase cell cultures of MGAS2221 and utilized two distinct methods to remove rRNA from our samples, the RiboZero kit from Epicenter, and the terminator- 5--Phosphate-Dependent Exonuclease (TEX). This gave us 4 distinct RNAs with which we performed RNAseq analysis. Both rRNA removal methods worked well, with only a small percentage of the final total read counts being derived from rRNA sequences. A single group A Streptococcus strain was investigated.

2013-03-20 | E-GEOD-45325 | biostudies-arrayexpress

RNA-seq analysis of Xenorhabdus nematophila

Project description:Analysis of size selected RNA samples to identify sRNAs using wild-type and rpoS mutant strains. Four experiments, two from each of two strains using two protocols.

2013-03-26 | E-GEOD-45298 | biostudies-arrayexpress

Computational Analysis of Bacterial RNA-Seq Data

Project description:RNA-seq analysis was carried out on N. gonorrhoeae grown in vitro to verify accuracy of a novel RNA-seq analysis program, Rockhopper Three replicates of N. gonorrhoeae grown in vitro

2013-03-26 | E-GEOD-45444 | biostudies-arrayexpress

Gene expression changes during overexpression of bacterial small RNA, DicF

Project description:Hundreds of small RNAs (sRNAs) have been identified in diverse bacterial species, and while the functions of most remain unknown, some regulate key processes, particularly stress responses. The sRNA DicF was identified over twenty-five years ago as an inhibitor of cell division, but since then has remained uncharacterized. DicF is 53 nucleotides and is encoded on a prophage (Qin) in the genomes of many Escherichia coli strains. Here, we performed RNA-Seq analyses of an E. coli strain with chromosomal deletion of dicF and overexpressing either empty plasmid or dicF from a plasmid. Systems analysis using computational methods identified additional mRNA targets of DicF: xylR and pykA mRNAs, encoding the xylose uptake and catabolism regulator and pyruvate kinase, respectively. We have further validated these target genes experimentally. RNA-Seq analyses was performed on E. coli strains overexpressing either the vector control or the small RNA DicF.

2016-01-16 | E-GEOD-76916 | biostudies-arrayexpress

Transcriptional control in Candidatus Pelagibacter ubique and other marine bacterial taxa

Project description:Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere. Bacteria were grown in batch culture and sampled twice during the initial, rapid phase of exponential growth and twice during the phase of slower growth that followed.

2015-03-03 | E-GEOD-66443 | biostudies-arrayexpress

RNA-seq analysis of Salmonella enterica Typhimurium LT2

Project description:We performed whole-genome transcriptomic analyses of the Salmonella Typhimimurium genome during glucose-phosphate stress. In particular, we wanted to elucidate the role of the the small RNA SgrS and protein regulator SgrT in the stress response.

2013-03-26 | GSE45445 | GEO

AroA deficient Salmonella Typhimurium â More than an auxotrophic mutant

Project description:Recombinant attenuated Salmonella are believed to act as powerful live vaccine carrier able to elicit protection against many infectious agents. âaroA exhibits auxotrophy for aromatic amino acids and is commonly used for attenuation. Interestingly, deletion of aroA dramatically increased virulence of the Salmonella. Detailed analyses demonstrate that Salmonellaâs physiology is significantly altered, most likely due to osmotic imbalance and stress. The result is a serious influence of lipid and amino acid turn over, possible increasing sensitivity to penicillin, complement and phagocytic uptake. In addition, in concert with other immunomodulating mutations, the phase of flagella expression is changed. Furthermore, virulence associated genes like arnT or ansB were affected. These alterations could explain the increased virulence. Thus, intravenous application of âaroA Salmonella to mice significantly increased induction of pro-inflammatory cytokines. We also employed such bacteria in therapy against tumors and realized that âaroA strains display an improved anti-tumor activity. The samples of Salmonella Typhimurium Wild type strain and derivates (SF100 (ÎlpxR9 ÎpagL7 ÎpagP8), SF101 (ÎaroA), SF102 (ÎlpxR9 ÎpagL7 ÎpagP8 ÎaroA)) were analyzed by RNA-seq. The control samples were cultivated in the LB medium until the exponential phase. Four biological replicas were pooled in pairs to get two replicas for RNA extraction, library preparation and sequencing. Tumor samples were collected from mice infected with Wt Salmonella and SF102. Bacterial RNA was extracted from single tumors. The tumor samples were split into two technical replicas for sequencing library preparation.

2016-08-09 | E-GEOD-74433 | biostudies-arrayexpress

RNA-seq of S. enterica serovar Typhimurium SL1344 and ∆acrB after 1, 3 and 5 hours of growth

Project description:The aim of this experiment was to determine changes in transcription profile of Salmonella SL1344 and SL1344 ∆acrB over the growth curve. Samples of both strains were taken after 1, 3 and 5 hours of growth (corresponding to early- and late-exponential phase and stationary phase) in LB media. Cells were harvested and RNA extraction, library preparation and sequencing using Illumina HiSeq were carried out by GENEWIZ Inc.

2021-09-28 | E-MTAB-9679 | biostudies-arrayexpress

Salmonella Typhiumurium LT2, wild type versus rfaC mutant.

Project description:Transcriptional analysis of rfaC mutant strain compared to an isogenic wild type strain Salmonella Typhimurium. Keywords: Genetic modification.

2010-01-14 | GSE19878 | 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