Xylella fastidiosa Study on different growth media
Ontology highlight
ABSTRACT:
ORGANISM(S): Xylella fastidiosa
SUBMITTER: Tiago Lopes
PROVIDER: E-GEOD-13748 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Transcriptome profiling by array of the Sinorhizobium meliloti GR4-derivative mutant GNS577, affected in ntrY and ntrX genes, to identify possible cell processes regulated by this system
2017-04-30 | E-MTAB-2511 | biostudies-arrayexpress
Project description:Pregnant rats (Long-Evans) were dosed perinatally with 0 or 6Â mg/kg/day of Aroclor 1254 from gestation day 6 through postnatal day (PND) 21. Gene expression in cerebellum and hippocampus from PND7 and PND14 animals was analyzed with an emphasis on developmental aspects. Changes in gene expression (>= 1.5 fold) in control animals identified normal developmental changes. These basal levels of expression were compared to data from Aroclor 1254-treated animals to determine the impact of gestational PCB exposure on developmental parameters. The results indicate that the expression of a number of developmental genes related to cell cycle, synaptic function, cell maintenance, and neurogenesis is significantly altered from PND7 to PND14. Aroclor 1254 treatment appears to dampen the overall growth-related gene expression levels in both regions with the effect being more pronounced in the cerebellum. Functional analysis suggests that Aroclor 1254 delays maturation of the developing nervous system, with the consequences dependent on the ontological state of the brain area and the functional role of the individual gene. Experiment Overall Design: Pregnant rats (Long-Evans) were dosed perinatally with 0 or 6Â mg/kg/day of Aroclor 1254 from gestation day 6 through postnatal day (PND) 21. Gene expression in cerebellum and hippocampus from PND7 and PND14 animals was analyzed with an emphasis on developmental aspects.
2009-09-23 | E-GEOD-13793 | biostudies-arrayexpress
Project description:Immunostimulatory CpG ODN trigger an innate immune response characterized by the rapid production of pro-inflammatory cytokines and chemokines, an effect that persists for days to weeks in vivo. Previous studies established that gene up-regulation is maximal 3 hr after CpG ODN treatment of normal mice {Klaschik et al. JLB 2009}. The immunostimulatory activity of CpG ODN is blocked by the addition of immunosuppressive ODN expressing multiple TTAGGG motifs. To clarify the mechanism underlying this suppression, changes in gene expresssion were evaluated by microarray in mice treated with 400 ìg of CpG ODN + 400 ìg of suppressive ODN. Data from 4 independent biological replicates/time point and treatment group and 6 untreated controls were used for all statistical analyses. A reference design was used. Reference cDNA vs. sample cDNA were hybridized to same array.
2011-06-01 | E-GEOD-22156 | biostudies-arrayexpress
Project description:[original title] Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome. In the present investigation we sought to refine the classification of urothelial carcinoma by combining information on gene expression, genomic, and gene mutation levels. For these purposes we performed gene expression analysis of 144 carcinomas, and whole genome array-CGH analysis and mutation analyses of FGFR3, PIK3CA, KRAS, HRAS, NRAS, TP53, CDKN2A, and TSC1, in 103 of these cases. Hierarchical cluster analysis identified two intrinsic molecular subtypes, MS1 and MS2, which were validated and defined by the same set of genes in three independent bladder cancer data sets. The two subtypes differed with respect to gene expression and mutation profiles, as well as with the level of genomic instability. The data shows that genomic instability was the most distinguishing genomic feature of MS2 tumors, and that this trait was not dependent on TP53/MDM2 alterations. By combining molecular and pathological data it was possible to distinguish two molecular subtypes of Ta and T1 tumors, respectively. In addition, we define gene signatures validated in two independent data sets that classify urothelial carcinoma into low (G1/G2) and high grade (G3) tumors as well as non-muscle and muscle-invasive tumors with high precisions and sensitivities, suggesting molecular grading as a relevant complement to standard pathological grading. We also present a gene expression signature with independent prognostic impact on metastasis and disease specific survival. We conclude that the combination of molecular and histopathological classification systems may provide a strong improvement for bladder cancer classification and produce new insights into the development of this tumor type. 144 bladder cancer tumor samples and 12 normal samples were analyzed on 2-color cDNA or oligo microarrays using the Stratagene Universal Human Reference RNA as the common reference sample. 24 samples are hybridized to both the cDNA and oligo platform and these were used for merging of data from the two different gene expression platforms into a single expression matrix and for subsequent evaluation steps. The merged gene expression matrix used for analyses is supplied as a supplementary file (at the foot of this record). 103 of the samples were also analyzed on a BAC array containing ~32 000 BAC clones. Arrays were produced at the Swegene Centre for Integrative Biology at Lund University (SCIBLU).
2010-06-14 | E-GEOD-19915 | biostudies-arrayexpress
Project description:CpG DNA interacts with TLR9 to stimulate a broadly protective innate immune response. This study uses bioinformatic network analysis of microarray data to identify the genes and regulatory networks triggered by CpG ODN. CpG treatment induced significant gene up-regulation (p < 0.00001) in the spleen within 30 min, peaking with the activation of >500 genes at 3 hr, and declining progressively thereafter. There were reproducible changes in the pattern of gene expression over time. This was mediated by a small group of “major inducers” (IL1A, IL1B, TNF, IFNG) whose activity was modulated by several “minor inducers” (NFKB1, IL6, IL15, IL18, STAT1, STAT2). The subsequent decline in gene activation was mediated by “suppressors” (MYC, IL1RN, SOCS1, SOCS3, NFKBIA, IL10, FOS) that actively down-regulated gene expression and targeted both major and minor inducers. Thus, the regulation of TLR9 dependent gene activation involves multiple waves of stimulation mediated by a small number of “major” and “minor” inducers followed by the active inhibition of gene expression by “suppressors”. Keywords: time series design Endotoxin-free phosphorothioate ODN were synthesized at the CBER core facility (FDA, Bethesda, MD) as previously described. Mice were injected intraperitoneal (i.p.) with 400 ìg of an equimolar mixture of CpG ODNs 1555 (GCTAGACGTTAGCGT) and 1466 (TCAACGTTGA) or control ODNs 1612 (GCTAGATGTTAGCGT) and 1471 (TCAAGCTTGA). Spleens were surgically removed from mice under sterile conditions after 0.5, 1, 3, 9, 24 hr, and/or 72 hr, diced, and stored at -800 C in RNAlater (Qiagen, Valencia, CA). Data from 4 independent experiments/time point and 4-6 untreated controls were used for all statistical analyses. Reproducibility was established by comparing gene expression profiles among similarly treated mice from independent experiments in mAdb (referenced above). Expression analyses were performed using BRB ArrayTools (Biometric Research Branch, NCI). Data were background corrected, flagged values were removed, spots in which both signals were <100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes (Yang et al., 2002). Analysis was restricted to genes present on >70% of the arrays after filtering. The gene expression profile of all treatment groups was compared to that of the control groups.
2009-04-01 | E-GEOD-11202 | biostudies-arrayexpress
Project description:CpG DNA binds to Toll-like receptor 9 to stimulate a strong innate immune response. Despite extensive studies of TLR9 mediated signal transduction, the scope of CpG-induced changes in gene expression is incompletely understood. In particular, the prolonged effects of CpG ODN (oligodeoxynucleotide) on gene activation have not been investigated despite evidence that a single dose of CpG ODN alters immune reactivity for several weeks. This study used gene expression analysis to monitor changes in mRNA levels for 14 days, and identified the genes, pathways, functional groups and regulatory networks triggered in vivo following CpG ODN administration. Two discrete peaks of gene activation (at 3 hr and 5 days) were observed after CpG administration. Both the regulation and function of genes activated during the second peak differed from those triggered shortly after CpG administration. Initial gene up-regulation corresponded to a period when TLR9 ligation stimulated genes functionally associated with the generation of innate and adaptive immune responses (e.g. the NF-kB and B-cell receptor pathways). The second peak reflected processes associated with cell division (e.g., cell cycle and DNA replication & repair). Whereas TNF and IFNG played central roles regulating the first peak of activation, E2F1, E2F2, BRCA1, and HRAS had major impact on the networks controlling the second peak. The complex bimodal pattern of gene expression elicited by CpG ODN administration provides novel insights into the long term effects of CpG DNA on genes associated with immunity and cell proliferation. Data from 4 independent biological replicates/time point (9 time points) and 6 untreated controls were used for all statistical analyses. A reference design was used. Reference cDNA vs. sample cDNA were hybridized to same array.
2010-05-16 | E-GEOD-16465 | biostudies-arrayexpress
Project description:We used RNA-seq to determine the effects of AraC and arabinose on RNA levels genome-wide in S. enterica. Wild-type or delta araC mutant cells were grown in both the presence and absence of 0.2% L-arabinose. RNA-Seq libraries from two independent biological replicate samples were sequenced for (i) wild-type cells with no treatment, (ii) wild-type cells treated with arabinose, (iii) delta araC cells with no treatment, (iv) delta araC cells treated with arabinose. Comparisons were made between (i) and (ii) [analysis file name: Salmonella RNA-seq processed WT without arabinose vs WT with arabinose.xls], between (i) and (iii) [analysis file name: Salmonella RNA-Seq proessed no arabinose WT vs no arabinose delta araC.xls], and between (ii) and (iv) [analysis file name: Salmonella RNA-Seq processed arabinose WT vs arabinose delta araC.xls]. All analysis files are available from https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1901/E-MTAB-1901.additional.1.zip
2013-10-04 | E-MTAB-1901 | biostudies-arrayexpress
Project description:Transcriptomic profiling of an rpoS mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown in nutrient broth supplemented with 1% glycerol to OD600=2.0-2.4 (early stationary phase). Two-condition experiment, the rpoS mutant compared to wild-type Pf-5 grown in nutrient broth supplemented with 1% glycerol to early stationary phase. There are three biological replicates and two flip-dye replicates for a total of six slides analyzed. Each slide contains three replicate spots per gene.
2012-12-31 | E-GEOD-38632 | biostudies-arrayexpress
Project description:The genome of the marine Synechococcus sp. WH8102 displays a minimal regulatory network yet physiological and molecular responses of this organism are tuned to episodic limitation for nitrogen and phosphorus. Microarray analyses have demonstrated a key role for the two-component regulatory system, PhoBR, in the regulation of P transport and metabolism in this strain. However, there is some evidence that another regulator, SYNW1019 (designated as ptrA), probably under the control of PhoB, is involved in the wider response to P-depletion. PtrA is one of only two genome encoded DNA binding proteins of the CRP family in Synechococcus sp. WH8102, and a potential transcriptional regulator with homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the precise role of this regulator we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-deplete growth conditions. During P-depletion the ptrA mutant failed to up-regulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is directly controlled by PtrA, including two phosphatase genes (SYNW0196, SYNW2390), a predicted phytase (SYNW0762) and a gene of unknown function (SYNW0165) all of which are highly up regulated during P-limitation. This result was confirmed by electrophoretic mobility shift assays which demonstrated binding of over expressed PtrA to promoter sequences upstream of the induced phosphatases (SYNW0165, SYNW0196 and SYNW2390). This work suggests a two-tiered response to P-depletion in this strain, the first being PhoB-dependent induction of high affinity PO4 transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly controlled by PtrA, including those involved in cell surface modification, metal uptake, photosynthesis, stress responses and other metabolic process, which may indicate a wider role for PtrA in cellular organisation. In an environmental context ptrA is found in a number of picocyanobateria isolated from a range of oceanic provinces, including strains that lack a functional phoBR..These results give broader insight into the regulation of physiological responses that may dictate niche adaptation in genetically diverse lineages of marine Synechococcus, and suggest that signalling networks and coordinated responses to nutrient availability are important, even in oligotrophic ocean environments. In this series gene expression of a ptrA mutant has been analyzed under phosphorus deplete conditions just after the onset of induction of phosphatase activity in wild type. There are six duel-channel slides upon which both ptrA mutant and wild type samples were hybridized. There are three technical replicates for each of two biological replicates including one flip-dye comparison. Each slide contains six replicate spots per gene.
2010-04-08 | E-GEOD-18511 | biostudies-arrayexpress
Project description:Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma 146 primary bladder cancer tumor samples were analyzed on BAC array containing ~32 000 BAC clones. Arrays were produced at the Swegene Centre for Integrative Biology at Lund University (SCIBLU).
2012-06-17 | E-GEOD-32535 | biostudies-arrayexpress