Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
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ABSTRACT:
PROVIDER: PRJNA156831 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Salmonella wild type in LB, 2mM indole until OD1 and 2mM indole for 15 minutes
| PRJNA171591 | ENA
Project description:Transcriptional profiling of Salmonella enterica serovar Typhimurium SL1344 cells comparing wildtype with ΔfabR mutant. Salmonella strains were cultured under free-living TSB conditions (TSB 1/20, 200 rpm, 25 °C) for 6h (ca. 2 x 108 cells/ml).
2014-12-31 | GSE52880 | GEO
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type grown to OD600=1 in LB alone or in LB supplemented with 2mM Indole, or with 2mM indole for 15 min (called shock). The goal is to determine Salmonella response to indole at different time points.
2013-01-30 | GSE39760 | GEO
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and deletion of the sdiA regulator-encoding gene grown to OD600=1 in LB alone or in LB supplemented with 2mM indole. The goal is to determine Salmonella response to indole and to define the SdiA-regulated genes in these conditions. 4 different conditions tested (wild type in LB, wild type in LB + 2mM indole, sdiA mutant in LB, sdiA mutant in LB + 2mM indole), 4 replicates for each condition. The reference on each hybridisation is the chromosomal DNA of the wild type strain.
2013-01-30 | E-GEOD-36805 | biostudies-arrayexpress
Project description:InvF ChIP-chip on Salmonella enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged InvF (IP samples) and wildtype strain (mock IP samples) Salmonella enterica serovar Typhimurium causes a range of diseases from self-limiting gastroenteritis to life-threatening systemic infections. Its complex infection process is initiated by the invasion of the intestinal epithelial monolayer by means of a type three secretion system. InvF is one of the key regulators governing the invasion of epithelial cells. By mapping the InvF regulon, i.e. locating its direct target genes, the gene network underlying invasion can be further examined, including identifying possible new effector-encoding genes. In order to map the InvF regulon, we performed chromatin immunoprecipitation combined with tiling microarray analysis (ChIP-chip) and compared expression of the identified target genes in an invF mutant and a wildtype strain. In addition, the promoter regions of these target genes were searched for the presence of an InvF recognition site. Finally, a query-driven biclustering method, combined with a microarray compendium containing publically available S. Typhimurium gene expression data, was applied as an in silico validation technique for functional relatedness between newly identified target genes and known invasion genes. As expected, under invasion inducing conditions, InvF activates the expression of invasion chaperone encoding sicA and the effector-encoding genes sopB, sopE, sopE2 and sopA by binding their promoter region. Newly identified InvF targets are steB, encoding a secreted effector, and STM1239. The presence of an InvF recognition site in the promoter regions of these target genes further supports this observation. In addition, the query-driven biclustering method revealed similarities in expression profiles between STM1239 and known InvF regulated invasion genes over a range of experimental conditions. In conclusion, we here deliver the first evidence for direct binding of InvF to the promoter regions of sopA and sopE2, and associate genes encoding a secreted effector (steB) and a putative novel effector (STM1239) with the Salmonella invasion regulator InvF.
2013-09-01 | GSE24062 | GEO
Project description:FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged FabR (IP samples) and wildtype strain (mock IP samples)
2014-12-31 | GSE52877 | GEO
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and deletion of the sdiA regulator-encoding gene grown to OD600=1 in LB alone or in LB supplemented with 2mM indole. The goal is to determine Salmonella response to indole and to define the SdiA-regulated genes in these conditions.
2013-01-30 | GSE36805 | GEO
Project description:The transcriptomes of Salmonella enterica serovar Typhimurium SL1344 and an isogenic acrF::aph mutant were compared.
2011-06-01 | E-MEXP-2976 | biostudies-arrayexpress
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type grown to OD600=1 in LB alone or in LB supplemented with 2mM Indole, or with 2mM indole for 15 min (called shock). The goal is to determine Salmonella response to indole at different time points. Different conditions were tested. The reference on each hybridisation is the chromosome DNA of the wild type strain. 4 replicates each for LB and LB + Indole, 6 replicates for indole shock.
2013-01-30 | E-GEOD-39760 | biostudies-arrayexpress
Project description:InvF ChIP-chip on Salmonella enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged InvF (IP samples) and wildtype strain (mock IP samples) Salmonella enterica serovar Typhimurium causes a range of diseases from self-limiting gastroenteritis to life-threatening systemic infections. Its complex infection process is initiated by the invasion of the intestinal epithelial monolayer by means of a type three secretion system. InvF is one of the key regulators governing the invasion of epithelial cells. By mapping the InvF regulon, i.e. locating its direct target genes, the gene network underlying invasion can be further examined, including identifying possible new effector-encoding genes. In order to map the InvF regulon, we performed chromatin immunoprecipitation combined with tiling microarray analysis (ChIP-chip) and compared expression of the identified target genes in an invF mutant and a wildtype strain. In addition, the promoter regions of these target genes were searched for the presence of an InvF recognition site. Finally, a query-driven biclustering method, combined with a microarray compendium containing publically available S. Typhimurium gene expression data, was applied as an in silico validation technique for functional relatedness between newly identified target genes and known invasion genes. As expected, under invasion inducing conditions, InvF activates the expression of invasion chaperone encoding sicA and the effector-encoding genes sopB, sopE, sopE2 and sopA by binding their promoter region. Newly identified InvF targets are steB, encoding a secreted effector, and STM1239. The presence of an InvF recognition site in the promoter regions of these target genes further supports this observation. In addition, the query-driven biclustering method revealed similarities in expression profiles between STM1239 and known InvF regulated invasion genes over a range of experimental conditions. In conclusion, we here deliver the first evidence for direct binding of InvF to the promoter regions of sopA and sopE2, and associate genes encoding a secreted effector (steB) and a putative novel effector (STM1239) with the Salmonella invasion regulator InvF. Three IP samples (from three biological replicates using anti-Myc antibody against Salmonella Typhimurium SL1344 strain encoding chromosomally 9Myc-tagged InvF) and three control mock IP samples (from three biological replicates using anti-Myc antibody against Salmonella Typhimurium SL1344 wildtype strain) were labeled with Cy5 and hybridized against a common genomic DNA reference, labeled with Cy3, on 6 S. Typhimurium LT2 whole genome tiling arrays
2013-09-01 | E-GEOD-24062 | biostudies-arrayexpress