Transcription profiling of Mycobacterium tuberculosis infected mice treated or non-treated with DNA-HSP65 vaccine treatment
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Generation III Array Scanner [Amersham]
ORGANISM(S): Mus musculus
DISEASE(S): Tuberculosis
SUBMITTER: Carlos Rodrigo Zarate Blades
PROVIDER: E-MEXP-944 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To gain insight into the changes in gene expression pattern upon Ebola infection, CD45+/+ (100% protein level) and CD45+/- (62% protein level) mice were challenged with mouse adapted Ebola virus. At time-points day 0, 1, 3, 5, 7, 9, 11 and 13, spleen tissue was harvested and splenocytes isolated. Total RNA was isolated for mRNA expression analysis. The mouse genome 430 2.0 array (Affymetrix, Inc.), which consists of over 39,000 genes in a single array, was used. Based on gene expression patterns, the variable genes were grouped into sixteen clusters. Each cluster contained genes associated with cellular immune processes, signaling, cell-cycle, complement coagulation cascade, biosynthesis/metabolism, ubiquitous genes involved in several cascades, and genes of unknown function. Interestingly, gene expression in clusters 2 and 3 were significantly downregulated by day 1 following EBOV challenge in CD45100% mice. In contrast, at day 1 following EBOV infection, the CD45 62% mice maintained gene expression patterns similar to day 0. The differences in gene expression patterns between the CD45 100% and CD45 62% splenocytes were less apparent at day 3 following infection and by days 5 and 7 they became very similar. At day 9, when wild-type mice had succumbed to the disease, the pattern in CD45 62% mice remained similar to the day 7 patterns of CD45 100% and CD45 62% mice. The pattern at days 11 and 13 in the CD45 62% mice had returned to that of day 0 CD45 100% or CD45 62% mice. These results suggested that in CD45 100% mice, subversion of the cell transcriptional machinery during the early stages of EBOV infection (day 1) might represent a major factor leading to death of the mice. In CD45 62% mice, early control of gene regulation likely provided the appropriate antiviral responses leading to regulated inflammation, immune co-stimulation, and survival. Experiment Overall Design: RNA expression in CD45 100% and 62% mice were compared at each time point: days 0, 1, 3, 5, and 7, using an empirical Bayes procedure. From 3 to 8 biological replicates were in each group. Samples for days 9, 11, and 13 (4 biological replicates each) were also available for only CD45 62%. Median expression values for highly variable genes within each group were clustered using agglomerative nesting over all available time points.
2009-09-05 | E-GEOD-17509 | biostudies-arrayexpress
Project description:Tracheal mucosal epithelial cells were scraped at 12 and 24 hours of infection, frozen in liquid nitrogen and stored at -80°C. The cells were sent to a biotechnology company for TMT quantitative proteomic analysis. The cells were sent to a biotech company for TMT quantitative proteomics analysis.
2024-01-26 | PXD044411 | Pride
Project description:We have used cDNA microarrays to compare gene expression profiles in brains from normal mice to those infected with the Anka strain of Plasmodium berghei, a model of cerebral malaria. For each of three brains in each group, we computed ratios of all quantifiable genes with a composite reference sample and then computed ratios of gene expression in infected brains with untreated controls. Of the almost 12,000 unigenes adequateluy quantified in all arrays, about 3% were significantly downregulated (p<0.05, >50% fold change) and about 7% were upregulated. Upon inspection of the lists of regulated genes, we identified a high number encoding proteins of importance to normal brain function or associated with neuropathology. These results emphasize the important impact of malarial infection on gene expression in brain and provide tentative target biomarkers that might provide novel therapeutic targets for neurological sequelae of disease. We have used a previously published protocol (Iacobas et al., Physiol Genomics 2005) and a composite reference RNA sample (R) prepared in sufficient quantity for the entire experiment from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females). This combination of source tissues provided a high diversity of genes expressed in the midrange of the detection system for the AECOM mouse cDNA microarrays. Briefly, 60μg total RNA, extracted in Trizol® (Invitrogen, Carlsbad, CA) from brains of three infected (I) and three control (C) mice, purified with RNeasy® mini kit (Qiagen, Valencia, CA), were reverse transcribed into cDNA incorporating fluorescent Cy3-dUTP. The composite reference was reverse transcribed to incorporate Cy5-dUTP. Each of the six Cy3-labeled brain extracts was co-hybridized overnight at 50°C against the Cy5-labeled reference with AECOM 32k Mouse oligonucleotide arrays, MO3 printing series (platform described in http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL5371). After hybridization, the slides were washed at room temperature, using solutions containing 0.1% sodium dodecyl sulfate (SDS) and 1% SSC (3M NaCl + 0.3M sodium citrate) to remove the non-hybridized cDNAs.
2010-09-16 | E-GEOD-24086 | biostudies-arrayexpress
Project description:Burkholderia pseudomallei can adapt to and thrive in a variety of environments, including soil and water, and also can infect different hosts, including humans, leading to the tropical disease melioidosis. Modulation of gene and protein expression is one of this pathogen's adaptive survival mechanisms, which could lead to changes in the bacteria's cell membrane, metabolism, and virulence. To better understand bacterial adaptation and host-pathogen interactions, this study compared the expression profiles of B. pseudomallei from infected mice to B. pseudomallei cultivated in soil extract media. B. pseudomallei in vivo was created by infecting mice through the intraperitoneal route and harvesting the spleens on day 5 post infection. Total RNA was isolated and sequenced from the harvested spleen. Sequence reads were mapped to the B. pseudomallei UKMD286 strain genome sequence.
2022-07-22 | E-MTAB-11200 | biostudies-arrayexpress
Project description:To investigate how chromatin is shaped during inflammation geared towards the development of fibrosis in peritoneal tissue, we performed ATAC-seq in peritoneal membranes from wt and Il-6 knockout mice challenged with SES (a lyophilized cell-free supernatant prepared from Staphylococcus epidermidis ) together with Th1 polarised CD4+ T-cells administered via the intraperitoneal route. Peritoneal membrane was harvested 3 hours after injection, immediately snap-frozen in liquid nitrogen, and stored at -80C until processed. Tissues were diced and ground to a fine powder with intermittent addition of liquid nitrogen and Omni-ATAC-seq was performed.
2022-04-04 | E-MTAB-10739 | biostudies-arrayexpress
Project description:Dysferlin is an essential muscle membrane repair protein and autosomal recessive mutations in its gene result in progressive muscular dystrophies collectively called dysferlinopathies. We previously showed that calpain-mediated cleavage within dysferlin exon 40a releases a 72kDa C-terminal minidysferlin recruited to injured sarcolemma. In the current study, we hypothesised that knocking out exon 40a will lead to defective membrane repair and development of muscular dystrophy over time. To address this hypothesis, we created three exon 40a knockout (40aKO) mouse lines with dysferlin protein levels ranging from ~80% of wildtype (WT) in 40aKO-3, ~50% in 40aKO-2 and ~10-20% in 40aKO-1 mice. Histopathological analysis of skeletal muscles harvested from all 12-month-old 40aKO mice showed little evidence of dystrophic features seen in dysferlin-null BLAJ mice. Lipidomics analysis on 18wk old quadriceps showed that all 40aKO lines had a similar lipidomic profile to WT and distinct from BLAJs. The proteomic profile of 40aKO lines was intermediate between that of WT and BLAJs. Laser membrane damage assays showed normal membrane repair capacity in all three 40aKO lines. These results collectively indicate that ~10-20% of dysferlin protein expression is sufficient for maintenance of the lipidome and membrane repair capacity, and crucially prevents development of muscular dystrophy.
2023-03-11 | PXD035918 | Pride
Project description:Proximity proteomics has greatly advanced the analysis of native protein complexes and subcellular structures in culture, but has not been amenable to study development and disease in vivo. Here, we generated a knock-in mouse with the biotin ligase (BioID) inserted at titin’s Z-disc region to identify protein networks that connect the sarcomere to signal transduction and metabolism. Our census of the sarcomeric proteome from neonatal to adult heart and quadriceps reveals how perinatal signalling, protein homeostasis and the shift to adult energy metabolism shape the properties of striated muscle cells. Mapping biotinylation sites to sarcomere structures refined our understanding of myofilament dynamics and supports the hypothesis that myosin filaments penetrate Z-discs to dampen contraction. Extending this proof of concept study to BioID fusion proteins generated with Crispr/CAS9 in animal models recapitulating human pathology will facilitate the future analysis of molecular machines and signalling hubs in physiological, pharmacological, and disease context.
2020-05-18 | PXD017341 | Pride
Project description:The Root-lesion nematode (RLN) Pratylenchus coffeae is a major ramie pest causing severe fiber yield loss annual in China. The response mechanism of ramie to RLN-infection is poorly understood. Two RLN-infected plants (Inf1 and Inf2) and two control plants (CO1 and CO2) were individually used to sequence by Illumina pair-end sequencing. About 56.3, 51.7, 43.4 and 45.0 million sequencing reads were generated from the libraries of CO1, CO2, Inf1 and Inf2, respectively. De novo assembly for these 196 million reads yielded 50,486 unigenes with an average length of 853.3 bp. Based on sequence similarity search with known proteins, a total of 24,820 (49.2%) genes were annotated for their function. Comparison of gene expression level between CO and Inf ramie based on the normalized value of read counts per kilobase of exon model per million reads (RPKM) revealed that there were 777 differentially expressed genes (DEGs). Further, these functional category of DEGs were classified by assigning them to gene ontology (GO) and clusters of orthologous group (COG). Pathway enrichment analysis showed that three pathways (Phenylalanine metabolism, Carotenoid biosynthesis and Phenylpropanoid biosynthesis) were severely influenced by RLN-infection. The genome-wide expression profiling of ramie responding to RLN-infection was first characterized. A series of candidate genes and pathways that may contribute to defense response against RLN in ramie will be helpful for further improving the resistance to RLN-infection. A total of four samples, two replicates of control plant (CO1 and CO2) and two replicates of RLN-infected plants (Inf1 and Inf2) were used for RNA-seq.
2014-04-28 | E-GEOD-51900 | biostudies-arrayexpress
Project description:Staphylococcus aureus pneumonia causes significant morbidity and mortality. Alpha-hemolysin (Hla), a pore-forming cytotoxin of S. aureus, has been identified through animal models of pneumonia as a critical virulence factor that induces lung injury. In spite of considerable molecular knowledge of how this cytotoxin injures the host, the precise host response to Hla in the context of infection remains poorly understood. We employed whole-genome expression profiling of infected lung to define the host response to wild-type S. aureus compared with an Hla-deficient isogenic mutant in experimental pneumonia. These data provide a complete expression profile at four and at twenty-four hours post-infection, revealing a unique response to the toxin-expressing strain. Gene ontogeny analysis revealed significant differences in the extracellular matrix and cardiomyopathy pathways, both of which govern cellular interactions in the tissue microenvironment. Evaluation of individual transcript responses to Hla-secreting bacteria was notable for upregulation of host cytokine and chemokine genes, including the p19 subunit of interleukin-23. Consistent with this observation, the cellular immune response to infection was characterized by a prominent TH17 response to wild-type staphylococci. These findings define specific host mRNA responses to Hla-producing S. aureus, coupling the pulmonary TH17 response to the presence of this cytotoxin. Expression profiling to define the host response to a single virulence factor proved to be a valuable tool in identifying pathways for further investigation in S. aureus pneumonia. This approach may be broadly applicable to the study of bacterial toxins, defining host pathways that can be targeted to mitigate toxin-induced disease. Animals were treated with PBS, S. aureus wild-type, or S. aureus Hla-deficient isogenic mutant.
2012-05-20 | E-GEOD-38053 | biostudies-arrayexpress
Project description:Using iTRAQ labeling and HPLC fractionation followed by high-resolution LC-MS/MS analysis, quantitative global proteome analysis was performed. In total, 6538 protein groups were identified from Triticum_aestivum, among which 2766 proteins were quantified.
2016-09-29 | PXD004564 | Pride