Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

QRT-PCR of ex vivo Salmonella enterica in NRAMP-1 minus/plus macrophage background

ABSTRACT: A major virulence factor in S. enterica is the pathogenicity island Spi2. The goal of the experiment was to determine the impact of the NRAMP-1 (natural resistance-associated macrophage protein-1) on expression of Spi2 in S. enterica wild type (WT) and triple mutant strain (TMS) with deletions in SPI-1 TTSS, SPI-2 TTSS, flagella. The stain 14028 was used for the experiment. Cells were grown in a NRAMP-1 wildtype (plus) or deleted (minus) macrophage background. Total RNA was extracted and processed by qRT-PCR. Two strains ( WT and TMS) grown under 2 conditions (NRAMP-1 wildtype (plus) or NRAMP-1 deleted (minus)) - total 4 samples were analyzed in the study. All PCRs were done in duplicates, located on the same PCR plate. For each duplicate the mean value was calculated and used as a data point for further normalization. We averaged the Cp values for all the data points in a sample and then subtracted this sample average Cp from all the data points of the sample. Only 192 primer pairs from 288 on the platform GPL11111 were used.

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

SUBMITTER: John Braisted

PROVIDER: E-GEOD-26806 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

qRT-PCR of ex vivo Salmonella enterica in TLR4 minus/plus macrophage background

Project description:A major virulence factor in S. enterica is the pathogenicity island Spi2. The goal of the experiment was to determine the impact of the toll-like receptor 4 (TLR-4) on expression of Spi2 in S. enterica wild type (WT) and triple mutant strain (TMS) with deletions in SPI-1 TTSS, SPI-2 TTSS, flagella. The stain 14028 was used for the experiment. Cells were grown in a TLR-4 wildtype (plus) or deleted (minus) macrophage background. Total RNA was extracted and processed by qRT-PCR. Two strains (WT and TMS) grown under 2 conditions (TLR-4 wildtype (plus) or TLR-4 deleted (minus)) - total 4 samples were analyzed in the study. All PCRs were done in quadruplicates, located on the same PCR plate. For each quadruplicates the median value was calculated and used as a data point for further normalization. A set of controls was selected for all data sets using the following criteria: the data points for the controls should have Cp <40 and be present in all the samples.

2011-06-13 | E-GEOD-26804 | biostudies-arrayexpress

qRT-PCR of ex vivo Salmonella enterica in TLR4 minus/plus macrophage background

2011-06-13 | GSE26804 | GEO

qRT-PCR of ex vivo Salmonella enterica in NRAMP-1 minus/plus macrophage background

Project description:A major virulence factor in S. enterica is the pathogenicity island Spi2. The goal of the experiment was to determine the impact of the NRAMP-1 (natural resistance-associated macrophage protein-1) on expression of Spi2 in S. enterica wild type (WT) and triple mutant strain (TMS) with deletions in SPI-1 TTSS, SPI-2 TTSS, flagella. The stain 14028 was used for the experiment. Cells were grown in a NRAMP-1 wildtype (plus) or deleted (minus) macrophage background. Total RNA was extracted and processed by qRT-PCR.

2011-06-13 | GSE26806 | GEO

Salmonella secretome analysis - Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants

Project description:Researchers identified effector proteins secreted into defined minimal medium designed to induce expression of the SPI-2 TTSS and its effectors. The secretome of the parent strain was compared to those of strains missing essential (ssaK::cat) or regulatory (ssaL) components of the SPI-2 TTSS. 20 known SPI-2 effectors were identified. To identify novel effector proteins, the secretome data was coupled with machine learning and 12 candidate proteins were selected for further characterization. Using CyaA reporter fusions, six novel type III effectors were identified and two additional proteins that were secreted into J774 macrophages independently of a TTSS were also identified.

2013-10-07 | PXD000391 | Pride

Serum miRNA profiles of patients with oral cancer and pre-cancer

Project description:The aim of this study was to examine the expression profiles of circulating miRNAs in the serum of patients with high-risk oral lesions (HRLs; oral cancer or carcinoma in situ) and to explore their utility as potential oral cancer biomarkers. Global serum miRNA profiles were generated by quantitative PCR method from 1) patients diagnosed with HRLs and undergoing intent-to-cure surgical treatment (N = 30) and 2) a demographically-matched, normal control group (N = 26). We next honed our list of serum miRNAs associated with disease by reducing the effects of inter-patient variability; we compared serum miRNA profiles from samples taken both before and after tumor resections (N = 10). Based on these analyses, fifteen miRNAs were significantly up-regulated and five were significantly down-regulated based on presence of disease (minimum fold-change >2 in at least 50% of samples, p < 0.05, permutation t-test). Five of these miRNAs (miR-16, let-7b, miR-338-3p, miR-223, and miR-29a) yielded an area under the ROC curve (AUC) >0.8, suggesting utility as non-invasive biomarkers for detection of oral cancer or high grade lesions. qPCR miRNA expression profiling of serum samples. The sample size for control and HRL cases are indicated in the summary. The samples were not processed in replicate. Dataset 1: Samples from pre-surgery HRL patients (N = 30) and normal controls (N = 26). Dataset 2: Samples taken both before and after tumor resections (N = 10). Processed separately from Dataset 1.

2013-04-15 | E-GEOD-37472 | biostudies-arrayexpress

Aeromonas hydrophila LC-MSMS - This project was designed to observe changes in proteins expression and toxicity proteins expression of Aeromonas hydrophila under normal and iron restriction conditions.

Project description:This project was designed to observe changes in proteins expression and toxicity proteins expression of Aeromonas hydrophila under normal and iron restriction conditions.

2018-02-16 | PXD007641 | Pride

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

Project description:Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of characterization in microbes other than Escherichia coli. Here, we have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (TraDIS), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrated a virulence and motility defect of a Salmonella ΔmgrB mutant and revealed an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Overall, our study highlights the power of interpreting available “omics” datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.

2020-12-07 | PXD018754 | Pride

Time series gene expression data from adult rat tail MNs following spinal cord transection

Project description:Spinal cord injury leads to impaired motor and sensory functions. After spinal cord injury there is a an initial phase of hypo-reflexia followed by a developing hyper-reflexia, often termed spasticity. Previous studies have suggested a relationship between the reappearance of plateau potentials in motor neurons and the development of spasticity after spinalization. To understand the molecular mechanism behind this phenomena we examined the transcriptional response of the motor neurons after spinal cord injury as it progress over time. We used a rat tail injury model where a complete transection of the caudal (S2) rat spinal cord leads to an immediate flaccid paralysis of the tail and a subsequent appearance of spasticity 2-3 weeks post injury that develops into strong spasticity after 2 months. Gene expression changes were studied in motor neurones 0, 2, 7, 21 and 60 days after complete spinal transection. Tail MNs were retrogradely labelled with Fluoro-Gold injected into the muscle and intra peritoneally. 5-7 days after tracer injections the spinal cord was dissected out, snap-frozen in liquid nitrogen, sliced in 10 um thick slices and fluorescent motor neurons were laser dissected into a collector tube to a total of ca. 50-200 cells pr sample. RNA was then extracted, two round amplified and hybridized to Affymetrix rat 230 2.0 arays. 31 samples were hybridized onto chips, 4 Spi-0 (Control), 6 Spi-2, 5 Spi-7, 8 Spi-21 and 8 Spi-60.

2010-05-27 | E-GEOD-19701 | biostudies-arrayexpress

IAH Salmonella infected chicken caecal contents

Project description:RNA from in vitro grown Salmonella typhimurium is compared with RNA extracted from Salmonella typhimurium from infected chick caecums using a common DNA reference. Keywords: Disease state analysis, infected versus uninfected, common reference Five replicates from infected chick caecal contents compared to a common reference. Three replicates from in vitro grown Salmonella compared to a common reference. The common reference was genomic DNA and always occupies the Cy3 channel (channel 2).

2010-05-26 | E-GEOD-10337 | biostudies-arrayexpress

Effect of hfq-deletion on Salmonella transcriptome

Project description:The expression profile of an S. Typhimurium hfq mutant-strain was compared to the parental strain under 2 different growth conditions; early stationary phase and SPI-1 (Salmonella pathogenicity island 1) inducing condition. Keywords: Genetic modification This study comprises two separate experiments performed under different growth conditions, were the gene expression profile was compared to that of the parental strain. Three biological replicates were performed for each strain and condition. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

2008-08-23 | E-GEOD-8985 | 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