Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cappable-seq analysis of the Salmonella Typhimurium SL1344 transcriptome with overexpression of MarA, SoxS, Rob or RamA

ABSTRACT: Cappable-seq was used to map transcription start sites globally in Salmonella Typhimurium SL1344. In addition to naturally occurring plasmids pSLT and pCol1B9, the cells carry derivatives of plasmid pAMNF, or pAMNM, that drive low level constitutive expression of epitope tagged MarA, SoxS, Rob or RamA derivatives.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

SUBMITTER: David Grainger

PROVIDER: E-MTAB-12628 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-seq analysis of MarA, SoxS, Rob and RamA biding across the Salmonella Typhimurium SL1344 genome

Project description:ChIP-seq data for Salmonella Typhimurium strain SL1344. The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies (for SoxS, Rob and RamA) or anti Myc (for MarA) antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.

2023-03-29 | E-MTAB-12627 | biostudies-arrayexpress

Cappable-seq analysis of the Salmonella Typhimurium SL1344 transcriptome

Project description:Cappable-seq was used to map transcription start sites globally in Salmonella Typhimurium SL1344. In addition to naturally occurring plasmids pSLT and pCol1B9, the cells carry plasmid pAMNF. The latter can be used for low level constitutive expression of a transcription factor of interest, though in these experiments no such ectopic transcription factor expression was used.

2023-05-03 | E-MTAB-12506 | biostudies-arrayexpress

Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis

2010-10-01 | GSE23417 | GEO

Transcriptome Sequencing of the RamA Regulon

2014-01-01 | GSE27197 | GEO

RamA as a global regulator for gene expression in Salmonella Typhimurium

2010-06-20 | GSE15485 | GEO

Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis

Project description:Mutation of marA, rob, and soxS causes a clinical strain of E.coli to be attenuated at d3 post-infection in a mouse model of pyelonephritis, here we extract RNA at d2 post infection to analyze transcriptional differences between the two strains. In order to purify enough bacterial RNA to perform microarray, we chose a time point (day 2 post-infection) just before the triple mutant begins to decrease in bacterial load. Mouse kidneys were extracted, homogonized, and samples were pooled in RNALater (Ambion) before extraction and analysis of the transcriptomes

2010-10-01 | E-GEOD-23417 | biostudies-arrayexpress

Transcriptome Sequencing of the RamA Regulon

Project description:We report the use of Illumina based transcriptome sequencing to determine the RamA Regulon in K. pneumoniae. This study has identified both genes and small RNAs that are upregulated in the presence of RamA. Comparison of genetically modified mutants; TS67 (delta ramA) and TS68 (delta ramR, ramA overexpresser)

2014-01-01 | E-GEOD-27197 | biostudies-arrayexpress

Different xenogeneic silencing strategies in Escherichia coli and Bacillus subtilis are dictated by RNA polymerase promiscuity

Project description:Cappable-seq was used to map transcription start sites globally in B. subtilis and E. coli to investigate spurious transcription, and how B. subtilis prevents it.

2022-01-12 | E-MTAB-10777 | biostudies-arrayexpress

Elucidating the RamA Regulon in Klebsiella pneumoniae

Project description:Directional RNAseq analyses was undertaken in Klebsiella pneumoniae Ecl8 and isogenic mutants Ecl8delta ramA and Ecl8delta ramR to determine the RamA regulon. All samples were grown in Luria Bertani broth until OD600 approx 0.6 prior to RNA extraction. Differential expression was determined using DEseq upon pairwise comparisons of Ecl8 vs Ecl8delta ramA, Ecl8deltaramA vs Ecl8deltaramR, Ecl8 vs Ecl8deltaramR.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2014-08-15 | E-ERAD-122 | biostudies-arrayexpress

RamA as a global regulator for gene expression in Salmonella Typhimurium

Project description:RamA, a 113-amino-acid regulatory protein, belongs to the AraC-XylS transcriptional activator family. Here, the network of genes regulated by RamA was investigated by determining changes in transcript profiles when ramA gene was knocked out from wild type LTL strain, which expresses ramA constitutively. Analysis used aerobic log-phase state RNA from S. Typhimurium strain LTL (ciprofloxacin MIC: 4 µg/ml) derived from S. Typhimurium LT2 by in vitro-induction using ciprofloxacin as control samples for comparison to the experimental samples taken from its mutant strain, LTLvramA with ramA-deletion. Six biological replicates were used for the experiment.Two replicates for each sample. One replicate per array.

2010-06-20 | E-GEOD-15485 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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