Transcription profiling of mouse Jardine SIDS Model
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: David Jardine
PROVIDER: E-MEXP-2189 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Gene expression analysis characterizes antemortem stress and has implications for establishing cause of death.
Jardine David D Cornel Leanne L Emond Mary M
Physiological genomics 20110621 16
Within the field of forensic pathology, determination of the cause of death depends upon identifying physical changes in the corpse or finding diagnostic laboratory abnormalities. When such perturbations are absent, definitive assignment of a cause of death may be difficult or impossible. An example of such a problem is sudden infant death syndrome (SIDS), a common cause of neonatal mortality that does not produce physical findings or laboratory abnormalities. Although respiratory failure as a c ...[more]
Similar Datasets
Project description:Proteome profiling was performed to investigate changes at a molecular level in the mouse corneal endothelium (CE) along with the basement membrane exposed to cigarette smoke (CS). Pregnant mice (gestation days 18-20) were placed in a whole-body exposure smoking chamber and a few days later pups were born. After 3½ months of CS exposure, the Confoscan4 scanning microscope was used to examine the CE of CS-exposed and control (Ct) mice. The CE was peeled under a microscope and maintained as four biological replicates (two male and two female) for CS-exposed and Ct mice; each replicate consisted of 16 CE. The proteome of the CE was investigated through mass-spectrometry using 8-plex isobaric tandem mass tags (TMT). The CE images of CS-exposed and Ct mice revealed a difference in the shape of corneal endothelial cells (CECs) accompanied by a nearly 10% decrease in CEC density (p = 3.0e-0.5) resulting from exposure to CS. The proteome profiling identified a total of 524 proteins exhibiting statistically significant changes in CE from CS-exposed and Ct mice. Importantly, proteins known to be an integral part of the basement membrane including COL4α1, COL4α2, COL4α3, COL4α4, COL4α5, and COL4α6, Col8α1, Col8α2, FN1, etc. exhibited diminished protein levels in the CE of CS-exposed mice. Here, we report the effects of CS on the CE, and our data strongly suggest that CS exposure results in reduced CEC density and diminished concentration of proteins known to be an integral part of the basement membrane.
2021-09-09 | PXD020036 | Pride
Project description:There is an emerging concern that particulate air pollution increases the risk of cranial nerve disease onset. Small nanoparticles, mainly derived from diesel exhaust particles reach the olfactory bulb by their nasal depositions. It has been reported that diesel exhaust inhalation causes inflammation of the olfactory bulb and other brain regions. However, these toxicological studies have not evaluated animal rearing environment. We hypothesized that rearing environment can change mice phenotypes and thus might alter toxicological study results. In this study, we exposed mice to diesel exhaust inhalation at 90 micro g/m3, 8 hours/day, for 28 consecutive days after rearing in a standard cage or environmental enrichment conditions. Microarray analysis found that expression levels of 112 genes were changed by diesel exhaust inhalation. Functional analysis using Gene Ontology revealed that the dysregulated genes were involved in inflammation and immune response. This result was supported by pathway analysis. Quantitative RT-PCR analysis confirmed 10 genes. Interestingly, background gene expression of the olfactory bulb of mice reared in a standard cage environment was changed by diesel exhaust inhalation, whereas there was no significant effect of diesel exhaust exposure on gene expression levels of mice reared with environmental enrichment. The results indicate for the first time that the effect of diesel exhaust exposure on gene expression of the olfactory bulb was influenced by rearing environment. Rearing environment, such as environmental enrichment, may be an important contributive factor to causation in evaluating still undefined toxic environmental substances such as diesel exhaust. RNA sample was taken from olfactory bulb of 56-day-old mouse received diesel exhaust (DE) inhalation at 90 micro g/m3, 8 hours/day, for 28 consecutive days, while control RNA was taken from mouse received clean air, after rearing in a standard cage or environmental enrichment conditions. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.
2013-04-18 | E-GEOD-46163 | biostudies-arrayexpress
Project description:The global gene expression of murine tooth germs dissected at various stages of tooth development was investigated. A list of genes differentialy expressed throughout the various time points was submitted to bioinformatic analysis using Ingenuity Pathway Analysis (IPA) to identify significant associations between clusters of genes found to be differentially expressed and signalling or canonical pathways or molecular/cellular functions. This approach was also used with clusters of genes isolated using the profile search function of Spotfire.). The study entailed a total of 58 dual-labeled/two-chanel microarrays.The results, encompassing at least triplicate microarray data at each time-point, were treated as single colored arrays. The resulting expression data was subsequently assembled into a single data file, facilitating analysis of the time-course of expression profiles of expressed genes.
2012-11-14 | E-MEXP-3581 | biostudies-arrayexpress
Project description:Isoprene is a well-studied volatile hemiterpene that protects plants from abiotic stress through mechanisms that are not fully understood. The antioxidant and membrane stabilizing potential of isoprene are the two most commonly invoked mechanisms. However, isoprene also affects phenylpropanoid metabolism, suggesting an additional role as a signaling molecule. In this study, microarray based gene expression profiling reveals widespread transcriptional reprogramming of Arabidopsis thaliana plants fumigated for 24 hrs with a physiologically relevant concentration of isoprene. Functional enrichment analysis of fumigated plants revealed enhanced heat- and light-stress-responsive processes in response to isoprene. Isoprene induced a network enriched in ERF and WRKY transcription factors, which may play a role in stress tolerance. The isoprene-induced upregulation of phenylpropanoid biosynthetic genes was specifically confirmed using quantitative reverse transcription polymerase chain reaction. These results support a role for isoprene as a signaling molecule, in addition to its possible roles as an antioxidant and membrane thermoprotectant. Plants were held at 23 °C for 24 hours and then held at 40 °C for 24 hours, either in the presence or absence of 20 PPM isoprene during the entire 48 hours. Leaf samples were taken at the end of both 24 hour treatment periods. Each of the 4 resulting conditions was replicated 3 times.
2015-09-01 | E-GEOD-72547 | biostudies-arrayexpress
Project description:The effect of chloroquine on mosquitoes transcript abundance was assayed by comparing gene expression between mosquitoes fed on a blood meal containing 50 mg/Kg of chloroquine and those that had fed on a normal blood meal. Pools of 50 midguts were dissected and were hybridize with MMC1 (or 20K) microarrays. <br><br>Anopheles gambiae female mosquitoes were blood fed on BALB/c mice infected with P. berghei and intraperitonally pre-treated with 50 mg/kg of chloroquine. As controls, mosquitoes were blood fed on untreated P. berghei infected mice.<br><br>Mosquitoes were collected 24 hours post-blood feeding and pools of 50 midguts were dissected and processed for hybridization with MMC1 (or 20K) microarrays.Two different biological experiments were performed for each treatment.
2007-10-12 | E-MEXP-1201 | biostudies-arrayexpress
Project description:An investigation of gene expression changes in rectal biopsies from donors with IBS compared to controls to begin to understand this complex syndrome. To further investigate differences between IBS groups (constipation and diarrhoea predominant) (part1) and how IBS relates to bacterial infection (part2) with biopsies taken 6 months after Campylobacter jejuni infection. Part1: 18 Constipation predominant IBS subjects (IBS-C) and 27 diarrhoea predominant IBS subjects (IBS-D) compared to 21 healthy volunteers (HV). Part2: 21 Campylobacter jejuni infection (PIBD, PIBS, PINIBS) compared to 19 healthy volunteers (HV). PIBD = post Campylobacter infection with IBS (within 6 months) PIBS = post infection IBS (unknown time point and organism) PINIBS = post Campylobacter infection with no resulting IBS
2012-07-12 | E-GEOD-36701 | biostudies-arrayexpress
Project description:The effect of fluoxetine on the proteome of synaptic fractions of cerebral cortex tissue of male Ts65Dn mice was compared to the effect in euploid mice.
2024-05-21 | PXD048722 | Pride
Project description:Inflammatory bowel diseases (IBD) in humans are characterized by chronic inflammation and gastrointestinal tissue damage, caused by a combination of genetic and environmental factors. It has been largely documented that IBD frequently lead to colorectal cancers (CRC). The identification of causative factors of IBD is thus essential to understand CRC progression and develop therapeutical approaches. Models have been described in which molecular alterations are combined with inflammatory treatments in order to recapitulate IBD-associated CRC. Here, we describe a mouse line, α6fl/fl Villin-Cre, in which inactivation of the gene encoding the integrin alpha-6 subunit (ITGA6) specifically in the intestinal mucosa results into chronic inflammation and intestinal carcinogenesis. In these mice, the loss of integrin alpha-6 beta-4, a receptor mediating the attachment of epithelial cells to laminins, leads to epithelial detachment, hyperplasia, chronic inflammation, rectal prolapses, and ultimately adenocarcinomas. Alterations of differentiation affecting mucus secreting (goblet) cells as well as changes in expression of essential intestinal transcription factors were detected. Thus alpha-6 beta-4 integrin is a key factor for the maintenance of intestinal integrity and its loss may represent a risk factor for tumor progression associated with IBD. Transcriptome analysis of RNA from normal versus inflamed and carcinomatous rectal mucosa of α6 integrin deficient intestinal epithelium mice was performed. RNAs were prepared from 5 adenocarcinomas, which were macrodissected from the rectal prolapses and 4 flanking inflamed rectal mucosa of 53-80 week-old α6fl/fl Villin-Cre mice. RNAs from normal rectal mucosa were obtained by rectum scraping from 4 matched control animals. The transcriptome analysis was performed using the Affymetrix Mouse Gene 1.0 ST arrays. Images were processed using affymetrix GeneChip® Command Console® Software (AGCC) (version 2.0) and numerical value were generated using Affymetrix Expression Console⢠Software (version 1.1).
2016-07-07 | E-GEOD-37749 | biostudies-arrayexpress
Project description:In previous work, cephalotaxine, harringtonine, homoharringtonine were shown to be accumulated differentially after various stimuli. Especially, after MeJA treatment, the concentration of 3 cephalotaxus alkaloids all showed decreasing. We speculated that the genes expressed lower after MeJA treatment might encode some enzymes responsible for the biosynthesis of cephalotaxus alkaloids. Therefore, choosing the sample treated with MeJA and the control sample for comparative iTRAQ analysis will greatly facilitate dissection of the genes involved in the biosynthesis of cephalotaxus alkaloids and even the acyl portions of cephalotaxus ester alkaloids. This approach is widely used for mining and identifying novel genes in the biosynthesis of secondary metabolites without genome data in plants.
2022-02-21 | PXD031354 | Pride
Project description:Developmental exposures play a role in adult onset chronic disease. The mechanisms by which environmental toxicants alter developmental processes predisposing individuals to chronic disease are not understood. arsenic exposure via drinking water causes cancer and cardiovascular disease. Transplacental arsenic exposure accelerates and exacerbates atherosclerosis in ApoE-knockout mice. The liver plays a central role in the interlinked diseases diabetes, metabolic syndrome and atherosclerosis. The hypothesis that accelerated atherosclerosis is a consequence of altered hepatic development was investigated by microarray profiling of mRNA and microRNA abundance in livers isolated from 10 week old (PND70) and newborn (PND1) mice exposed or not exposed to arsenic from day 8 post-fertilization to birth. The results show that arsenic exposure alters the trajectory of both mRNA and microRNA expression as mice age. A 51-gene signature of arsenic exposure in both PND1 and PND70 mice was identified. Pathway Architect analysis of this signature identified nodes of interaction including Hspa8, IgM and Hnf4a. Gene ontology analysis of arsenic exposure-altered mRNAs indicated that pathways for gluconeogenesis and glycolysis were suppressed in PND1 mice and pathways for protein export, ribosome, antigen processing and presentation, and complement and coagulation cascades were induced in PND70 mice. Analysis of promoters of differentially expressed genes identified enriched transcription factor binding sites and cluster analyses revealed groups of genes sharing sets of transcription factor binding sites suggesting common regulation. Srebp1 binding sites are present in ~1/6 of the genes differentially expressed in PND70 livers. Western blot analyses of PND70 liver proteins showed that the inducible form of heat shock protein 70 (Hspa1, Hsp70) and the active form of Srebp1 were induced in arsenic-exposed mice as were plasma AST and ALT levels. These results suggest that transplacental ar Samples from three frozen livers from each group (newborn exposed and unexposed, 10 week old exposed and unexposed), and from separate litters, were homogenized and total RNA purified using mirVANA RNA pufification kits (Ambion, Carlsbad, CA). RNA was quantitated and intergrity determined on a Nanochip using a Bioanalyzer (Agilent, Santa Clara, CA). Microarray analyses for miRNAs abundance in total liver RNAs was performed by Exiqon (Woburn, MA) using two-color design against mouse standard total RNA (Ambion, now part of Applied Biosystems) and Exiqon LNA 1500 microarrays. Microarray analyses for mRNA abundance was performed using 2 color design against mouse standard total RNA (Stratgene, LaJolla, CA) and 44k arrays produced at the NIA . The processed data on Exiqon LNA-1500 are attached as a Series supplementary file. The data are based on the same samples as described in Agilent data submitted here. The supplementary data includes only the murine miRNA data on the array because these are the only data supplied by Exiqon. The relationship between GEO's sample names here (Agilent data) and column heads of spreadsheets (Exiqon data) are described in the first sheet of supplemental file: Project_Summary_Report_Heather_Miller_01042009_MTE.xls
2012-06-21 | E-GEOD-30783 | biostudies-arrayexpress