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

Transcription profiling of Salmonella enterica (I) serovar Typhi Ty2 wild type and ompR null strains in a strand-specific manner

ABSTRACT: Analysis of transcriptome in a strand-specific manner to further refine previous genome annotation; RNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi ompR regulon and identify novel ompR regulated transcripts.

ORGANISM(S): Salmonella enterica

SUBMITTER: Maria Fookes

PROVIDER: E-TABM-644 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Salmonella enterica serotype SL1344 wildtype, pSf-R27sfh and pSf-R27 at stationary and exponential growth phases, to investigate the role of the Sfh protein encoded by transmissible plasmids and involved in human typhoid

Project description:The Sfh protein is encoded by self-transmissible plasmids involved in human typhoid and is closely related to the global regulator H-NS. We have found that Sfh provides a stealth function that allows the plasmids to be transmitted to new bacterial hosts with minimal effects on their fitness. Introducing the plasmid without the sfh gene imposes a mild H-NS- phenotype and a severe loss of fitness due to titration of the cellular pool of H-NS by the A+T-rich plasmid. This stealth strategy seems to be used widely to aid horizontal DNA transmission and has important implications for bacterial evolution.

2007-01-15 | E-SGRP-7 | biostudies-arrayexpress

Transcription profiling of wild type and ZakA and GskA knock-out Dictyostelium discoideum to investigate the Zak1-GSK-3 signalling pathway

Project description:GskA, the Dictyostelium GSK-3 orthologue, is modified and activated by the dual-specificity tyrosine kinase Zak1 and the two kinases form part of a signalling pathway that responds to extracellular cAMP. We identify potential cellular effectors for the two kinases by analysing their null mutants. There are proteins and mRNAs that are altered in abundance in only one or other of the two mutants, indicating that each kinase has some unique functions. However, proteomic and micro-array analysis respectively identified 3 proteins and 37 genes that are similarly mis-regulated in both mutant strains. The positive correlation between the array data and the proteomics data is consistent with the Zak1-GskA signalling pathway functioning by directly or indirectly regulating gene expression. The discoidin 1 genes are positively regulated by the pathway while the abundance of the H5 protein is negatively regulated. Two of the targets, H5 and discoidin 1, are well-characterised markers for early development, indicating that the Zak1-GskA pathway plays a role in development earlier than previously observed.

2007-10-24 | E-SGRP-4 | biostudies-arrayexpress

Transcription profiling of Dictyostelium discoides mutant cell type aspidocyte induced by heavy meatals and antibiotics

Project description:We describe the serendipitous discovery and first characterization of a new resistant cell type from Dictyostelium, which we propose to call the aspidocyte (aspida: Greek for shield). These cells are induced from amoebae by a range of toxins including heavy metals and antibiotics, and were first detected by their striking resistance to detergent lysis. Aspidocytes are separate, rounded or irregular shaped cells that are immotile but remain fully viable; once the toxic stress is removed, they revert to amoeboid cells within an hour. Induction takes a few hours and is completely blocked by the protein synthesis inhibitor cycloheximide. Aspidocytes lack a cell wall and their resistance to detergent lysis is active, requiring continued energy metabolism, and may be assisted by a complete cessation of endocytosis, as measured by uptake of the dye FM1-43. Microarray analysis shows that aspidocytes have a distinct pattern of gene expression with a number of genes up-regulated that are predicted to be involved in lipid metabolism. Aspidocytes were initially detected in a hypersensitive mutant, in which the AMP deaminase gene is disrupted, suggesting that the inductive pathway involves AMP levels or metabolism. Since aspidocytes can also be induced from wild-type cells and are much more resistant than amoebae to a membrane disrupting antibiotic, it is possible that they are an adaptation allowing Dictyostelium cells to survive a sudden onslaught of toxins in the wild.

2007-02-06 | E-SGRP-5 | biostudies-arrayexpress

Transcription profiling of three human colorectal adenocarcinoma cells lines two which are mismatch repair deficient to characterize the post-transcriptional profile

Project description:characterize the post-transcriptional profile of mismatch repair-deficient colon cancer

2008-07-15 | E-MEXP-1696 | biostudies-arrayexpress

Chromatin immunoprecipitation of the MSL-1 and MSL-3 vs a mock IP in Drosophila and transcription profiling of X linked genes in WT male or female III instar larvae to provide X chromosome wide profiling of MSL-1 distribution and dosage compensation in Drosophila

Project description:Dosage compensation ensures that males and females, despite unequal number of X chromosomes, equalize for X linked gene expression. In Drosophila, it is achieved by a two-fold up-regulation of most of the genes present on the male X chromosome, and requires the association of the Dosage Compensation Complex (DCC) on the X chromosome. One of the main intriguing aspects of dosage compensation is how this complex is able to target specifically hundreds of sites only on the X chromosome in order to ensure dosage compensation. In order to better understand the targeting of the DCC and the dosage compensation mechanism, we have then decided to analyze the distribution of the DCC as well as the expression levels in male and female in a more complete and precise manner, using microarrays. In this experiment, we present the data used to analyse the distribution of the MSL-1 and MSL-3 protein (part of the DCC complex) on the X chromosome in WT embryos aged from 0H-14H, as well as the distribution of MSL-1 in embryos aged from 4-6H and in male III instar salivary glands. The DNA amplified from the specific immunoprecipitation (MSL-1 or MSL-3 IP) were labelled using Cy5-dCTP and hybridized against DNA amplified from a non specific immunoprecipitation (mock IP), labeled with Cy3 dye. In parralel we present the data used to analyse the expression profile of X-linked genes in WT male or female III instar larvae salivary glands. The cDNA amplified from the RNA extracted from the male or female salivary glands were labelled using Cy5-dUTP and hybridized against the reference sample, labelled with Cy3-dUTP (pool RNA from ON embryos, adultes, and salivary glands mixed at a ratio 1:1:1.and amplified as the RNA from salivary glands). We used for this study a cDNA array developed by the Genecore facility in EMBL, covering the DGC1 and DGC2 cDNA libraries from the Berkeley Drosophila Genome Project, which represents more than 70% of the coding Drosophila genome.

2006-04-01 | E-MEXP-554 | biostudies-arrayexpress

Transcription profiling of Ky mouse mutant soleus muscles vs wild type soleus muscles

Project description:A comparison of Ky mouse mutant soleus muscles versus wildtype soleus muscles. Hybridisation of 3 Mouse SGC 7.5k oligo slides, using 3 independent pools of 10 mice (5 male, 5 female)for both WT and mutant animals.

2005-11-10 | E-MEXP-481 | biostudies-arrayexpress

Transcription profiling of 13.5dpc embryonic gonad/mesonephros from male Mrotm1H/Mrotm1H mice vs male wild type littermates

Project description:Direct comparison of gene expression in 13.5dpc embryonic gonad/mesonephros between male Mrotm1H/Mrotm1H mice and male wild-type littermates. Two independent pools of 10 gonads (5 mice) were compared on 4 microarrays (two colourswaps).

2007-01-09 | E-MEXP-527 | biostudies-arrayexpress

miRNA chronic OVA aerosol

Project description:specific pathogen-free female BALB/c mice aged 7-8 weeks (Animal Resources Centre, Perth, Western Australia) were systemically sensitised by intraperitoneal injection of 50 M-5g of alum-precipitated chicken egg OVA (Grade V, ?98% pure, Sigma Australia) 21 and 7 days before inhalational challenge, then exposed to aerosolised OVA in a whole body inhalation exposure chamber (Unifab Corporation, Kalamazoo, MI). Chronic low-level challenge involved exposure to ?3 mg/m3 aerosolised OVA for 30 minutes/day on 3 days/week for up to 6 weeks. Particle concentration within the chamber was continuously monitored using a DustTrak 8520 instrument (TSI, St Paul, MN). All experimental procedures complied with the requirements of the Animal Care and Ethics Committee of the University of New South Wales (reference numbers: 06/119B and 08/09B). Mice were sacrificed after 1,2,4 and 6 weeks of OVA exposure. Control groups included naM-ove mice and mice that were not sensitised but were challenged for 6 weeks with aerosolised OVA.

2011-06-10 | E-MEXP-3118 | biostudies-arrayexpress

Transcription profiling of mouse Ostesy mutant soleus muscles vs wild type soleus muscles.

Project description:A comparison of Ostesy mutant soleus muscles to wildtype soleus muscles. Hybridisation of 3 Mouse SGC 7.5k oligo arrays, using 3 pools of 10 mice(5 male and 5 female) for mutant and WT.

2007-12-10 | E-MEXP-482 | biostudies-arrayexpress

OJeanJean_eRF3a_ATF4

Project description:We previously showed that eRF3a depletion in the human colon carcinoma cell line HCT116 p53+/+ induces mTOR signaling pathway inhibition (Chauvin et al., 2007) suggesting that eRF3a belongs to a regulatory mechanism that modulate mTOR activity. However, this mechanism and the precise role of eRF3a remain to be determined. Here, to elucidate the mechanism dictating mTOR signaling pathway inhibition, we aimed to define the transcript expression and polysome profiles of HCT116 cells after short interfering RNA (siRNA)-mediated depletion of eRF3a. Three days after HCT116 cells electroporation with either sh-3a1 which was previously shown for effectively silence eRF3a (Chauvin et al., 2005) or control shRNA (sh-Ctrl), total and polysome-associated RNAs were extracted and we conducted a microarray analysis of differentially expressed genes using the Illumina HumanHT-12 Expression BeadChips.

2012-08-30 | E-MEXP-3512 | 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