Differential Expression Studies in Murine Splenic Cells During Prion Infection
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Rhiannon Huzarewich
PROVIDER: E-GEOD-17446 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Polygalacturonase-inhibiting proteins (PGIPs) in plant cell walls inhibit fungal endopolygalacturonases (ePGs). Their action directly limits the effective ingress of the pathogen and is thought to lead to an up-regulated defense response. We previously showed that, PGIP activity, ePG inhibition and decreased Botrytis cinerea susceptibility were correlated in tobacco plants over-expressing grapevine (Vitis vinifera) Vvpgip1. In order to evaluate the base-line impact of PGIP over-expression, the transcriptome and hormone profiles of two transgenic lines with characterized resistance phenotypes were investigated in the absence of pathogen infection. Three microarray slides in total were hybridized: two slides using Vvpgip1 line 37 and WT, with a dye swap included to account for dye bias; and one slide using Vvpgip1 line 45 as test and WT as reference.
2011-12-08 | E-GEOD-26324 | biostudies-arrayexpress
Project description:Streptococcus sanguinis is a major component of the oral flora and an important cause of infective endocarditis. The genome sequence of S. sanguinis strain SK36 was recently determined. A number of foreign genes acquired by natural transformation were detected, as well as orthologs of competence genes previously identified in other species. However, significant differences in the S. sanguinis competence system relative to that of other streptococci were noted. We sought to examine S. sanguinis genetic competence, to characterize the global transcriptional response to competence induction, and to compare our results with those obtained from previous analyses of other streptococci. A mutant possessing an in-frame deletion in the comC gene encoding the competence-stimulating peptide was created and confirmed to have the expected phenotype. Studies indicated that competence could be induced in this strain by addition of competence-stimulating peptide, and determined the optimal conditions to employ for this purpose. Expression was monitored by microarray analysis at multiple time points from 2.5 to 30 min after induction. Over 200 genes were identified whose expression was altered at least two-fold in at least one time point, with the majority upregulated. The M-bM-^@M-^\lateM-bM-^@M-^] response was typical of that seen in previous studies. However, comparison of the M-bM-^@M-^\earlyM-bM-^@M-^] response in S. sanguinis with that of other streptococci revealed unexpected heterogeneity with regard to the number of genes induced, the nature of these genes, and their putative upstream regulatory sequences. S. sanguinis possesses a comparatively limited early response, which may define a minimal competence regulatory circuit. Transcriptional analysis of S. sanguinis strain JFP41 cells 0 to 30 min after treatment with CSP. Biological replicates: 3 replicates each independently grown and harvested. 4 technical replicates per array
2011-01-21 | E-GEOD-21619 | biostudies-arrayexpress
Project description:C. albicans (strain CAI4-CIp10) was grown according to CRISP SOP. An overnight culture was started from a single colony in YPD-Tris,(100mM Tris.HCl) pH 7.4 and incubated overnight at 30C in shaking incubator. The next day, 500 ul culture was inoculated into 50 ml YPD-Tris, pH 7.4. The following day a fresh culture was inoculated in YPD-Tris to an OD600 of 0.2 and grown to OD600 of 0.8 at 30C in a shaking incubator. At this point the culture was split, diluted back to OD600 of 0.2 in fresh medium and stress agents added at time =0 (XS = 5mM H2O2, OS = 1M NaCl or a combination, OSXS). After 10 min the cultures were harvested by centrifugation and cell pellets flash frozen in liquid nitrogen. Three independent cultures were grown for RNA extraction for each isolate at each condition.<br><br>The control sample was obtained from cells with no stress agents added, harvested at time=0. RNA was extracted and transcript profiling carried out by microarray analysis using custom microarrays (Eurogentec).
2014-07-01 | E-MEXP-3003 | biostudies-arrayexpress
Project description:A pre-culture in NGY (overnight 30M-0C) was used to inoculate RPMI-1640 medium to an initial optical density at 600 nm (OD600) of 0.05. Cells were then grown to mid exponential phase (OD600 = 0.5M-^V0.6) at the appropriate temperature (25M-0C or 35M-0C) before the culture was<br><br>split into two aliquots and fluconazole (32 ?g mlM-^V1 final concentration) added to one; the other serving as the control. After 2 h the cells were harvested by centrifugation and flash<br><br>frozen in liquid nitrogen. Three independent cultures were grown for RNA extraction for each isolate at each condition. RNA was prepared from cell pellets with TRIZOLM-. reagent (Invitrogen) and a mechanical disruption method.
2011-11-16 | E-MEXP-3000 | biostudies-arrayexpress
Project description:A green fluorescence protein (GFP)-derived dsRNA (dsRNA-GFP) has been used as an exogenous control for Apis mellifera RNAi assays by multiple research groups. Its sequence does not share any significant homology with any known honey bee genes. Although dsRNA-GFP is not expected to trigger an RNAi response in treated bees, undesirable effects on gene expression, pupal pigmentation or developmental timing have been routinely observed. To better understand the multiple molecular and phenotypic effects of dsRNA-GFP in honey bees and to evaluate its use as a control for RNAi studies, we examined the impact of dsRNA-GFP on global gene expression patterns in developing workers. We found that dsRNA-GFP causes large-scale changes in gene expression associated with multiple biological processes. Furthermore, dsRNA-GFP exposure tended to preferentially decrease, rather than increase, expression of genes compared to controls. Gene expression differences were analyzed using a dye-swap design. Second instar worker larvae received 0.5 M-NM-<g of dsRNA-GFP. Non-treated and dsRNA-GFP treated 7 day-old workers (W7d) were sampled.
2013-01-10 | E-GEOD-41004 | biostudies-arrayexpress
Project description:The regulation of complex cellular activities in palmitate treated HepG2 cells, and the ensuing cytotoxic phenotype, involves cooperative interactions between genes. While previous approaches have largely focused on identifying individual target genes, elucidating interacting genes has thus far remained elusive. We applied the concept of information synergy to reconstruct a ?gene-cooperativity? network for palmititate-induced cytotoxicity in liver cells. Our approach integrated gene expression data with metabolic profiles to select a subset of genes for network reconstruction. Subsequent analysis of the network revealed insulin signaling as the most significantly enriched pathway, and desmoplakin (DSP) as its top neighbor. We determined that palmitate significantly reduces DSP expression, and treatment with insulin restores the lost expression of DSP. Insulin resistance is a common pathological feature of fatty liver and related ailments, whereas loss of DSP has been noted in liver carcinoma. Reduced DSP expression can lead to loss of cell-cell adhesion via desmosomes, and disrupt the keratin intermediate filament network. Our findings suggest that DSP expression may be perturbed by palmitate and, along with insulin resistance, may play a role in palmitate induced cytotoxicity, and serve as potential targets for further studies on non-alcoholic fatty liver disease (NAFLD). free fatty acids(palmitate, oleate, linoleate) 0.7mM and tnf-alpha (0 20,100 ng/ml) were subjected to HepG2 cell line to study the cytotoxicity induced by these two factors. control(Hepg2 medium and BSA medium) treatment(combinations of TNFa+FFAs) two biological replicates for each condition, color swap for each sample
2012-05-01 | E-GEOD-26885 | biostudies-arrayexpress
Project description:WD40 motif-containing Msi1-like (MSIL) proteins play pleiotropic cellular functions as a negative regulator of the Ras/cAMP-pathways and a component of chromatin assembly factor-I (CAF-I), and yet have not been studied in fungal pathogens. Here we identified and characterized an MSIL protein, Msl1, in Cryptococcus neoformans, which can cause fatal meningoencephalitis in humans. Notably, Msl1 was not a functional ortholog for the yeast Msi1 but played pleiotropic roles in C. neoformans in both cAMP-dependent and -independent manners but mainly Ras-independently. Msl1 negatively controlled antioxidant melanin production and sexual differentiation, which can be repressed by inhibiting the cAMP-signaling pathways. In contrast, Msl1 controlled thermotolerance, diverse stress responses, and antifungal drugs resistance in Ras/cAMP-independent manners. Cac2, which is the second CAF-I component, appeared to play both redundant and distinct function with Msl1. Msl1 is required for full virulence of C. neoformans. Transcriptome and proteomic analysis identified a group of Msl1-regulated genes or -interacting proteins, respectively, which mostly include stress-related genes, including HSP12, HSP78, SSA1, SSA4, and STM1. Furthermore, we identified the third putative component of CAF-1, Rlf2, in C. neoformans. In conclusion, this study demonstrated the pleiotropic roles of Msl1 in human fungal pathogen C. neoformans, providing a novel antifungal therapeutic target. There is more than 95% genome homology between JEC21 and H99. Therefore, 6 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligos are used in this analysis. Total RNAs are extracted from 2 strains from H99 (H99 wild-type strain (Cryptococcus neoformans var. grubii serotype A), msl1M-NM-^T). 3 biological replicate experiments are performed for each strain. We use the mix of all total RNAs from this experiment as the control RNA. We use Cy3 as the test sample dye and Cy5 as the control dye.
2012-08-23 | E-GEOD-40303 | biostudies-arrayexpress
Project description:Two sets of microarray experiments examining the transcriptional response to Ni deprivation. One set was for growth on ammonium and the other for growth on urea Pairwise replicated comparisons (Ni deprivation in urea and ammonia)
2012-08-08 | E-GEOD-39972 | biostudies-arrayexpress
Project description:Measurement of changes in the mRNA transcript abundance of 1709 cDNAs in Xerophyta humilis leaves at 6 relative water contents (RWC) (100%, 80%, 60%, 40%, 20% and 5%RWC respectively). 3105 cDNA clones (corresponding to 1709 unique cDNAs) were randomly selected from X. humilis cDNA libraries (Leaf Dehydration (LD), Leaf Rehydration (LR), Root Dehydration (RD) and Root Rehydration (RR)), amplified by PCR, and printed on each glass slide multiple times (ranging from 4 to 12X), such that each printed block contained a random unbiased mixture of cDNAs from the 4 different cDNA libraries. Total RNA extracted from each X. humilis leaf sample was linearly amplified, labelled with Cy3, and simultaneously hybridized with Cy5 labelled common reference RNA, to the printed cDNA arrays. The reference RNA comprised equal amounts of total RNA pooled from 6 different RWC experimental samples. Data was recorded for five biological replicates for each of the 6 RWC stages being investigated.
2012-03-29 | E-GEOD-34952 | biostudies-arrayexpress
Project description:BACKGROUND: Lithospermum erythrorhizon, popularly known as Gromwell, is a perennial herb belonging to the family of Boraginaceae and its extract is known to have diverse pharmacological, cosmetic, and nutritional values for human. Nevertheless the biological influence of Gromwell extract on general physiology of eukaryotic cells remains unknown. In this study, we for the first time performed a global transcriptome analysis by using DNA microarray analysis to identify genes affected by the addition of Gromwell extract (GE) by using a eukaryotic microorganism, basidiomycete fungus Cryptococcus neoformans, as a model system. RESULTS: The transcriptome analysis revealed that a total of 1932 genes are differentially regulated in a statistically significant manner and expressions of 715 genes are up- (315 genes) or down-regulated (457 genes) more than twofold upon GE treatment. In response to GE treatment, genes involved in signal transduction genes are immediately regulated and the evolutionarily conserved set of genes involved in the core cellular functions, including DNA replication, RNA transcription/processing, and protein translation/processing, are generally upregulated. In contrast, a number of genes involved in carbohydrate metabolism and transport, inorganic ion transport and metabolism, post-translational modification/protein turnover/chaperone functions, and signal transduction are downregulated by the GE treatment. Among the GE-responsive genes that are also evolutionarily conserved in the human genome, we confirmed expression patterns of YSA1, TPO2, FET5 (CFO1), and PZF1 by Northern blot analysis. Based on the functional characterization of some GE-responsive genes through phenotypic analysis of gene knockout mutants, we found that GE treatment may promote cellular tolerance against a variety of environmental stresses in eukaryotes. CONCLUSIONS: A significant portion of the Cryptococcus genome is affected in expression levels by treatment of GE, implying that the general physiology of eukaryotic cells is significantly affected by the GE treatment. There are more than 95% of genome homology between JEC21 and H99. Therefore 6 slides of JEC21 (Cryptococcus neoformans var. neoformans serotype D) 70-mer oligo are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted from H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A)) with 6.4 mg/ml Gromwell extract in 0, 10, 30, 60 min. We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy3 as Sample dye and Cy5 as a control dye.
2013-01-10 | E-GEOD-43370 | biostudies-arrayexpress