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E-MEXP-338
Rattus norvegicus
6 Downloadable Samples
Affymetrix Rat Expression 230A Array (rae230a)
Description
We have compared the gene-expression in cerebral arteries from rats after experimental SAH with the expression in cerebral vessels from sham operated animals. The model is well characterised (Prunell et al. 2003; Prunell et al. 2004) regarding the physiological changes but not regarding the gene expression pattern. Male Sprague-Dawley rats (350-400 g) were anaesthetized using 5% halothane (Halocarbon Laboratories, River Edge, New Jersey) in N2O/O2 (30:70). The rat was intubated and artificially ventilated with inhalation of 0.5-1.5% halothane in N2O/O2 (70:30) during the surgical procedure. The depth of anaesthesia was carefully monitored and the respiration checked by regularly withdrawing arterial blood samples for blood gas analysis (Radiometer, Copenhagen, Denmark). An arterial catheter to measure blood pressure was placed in the tail artery and a catheter to monitor intracranial pressure (ICP) was placed in the subocciptal membrane. At either side of the skull, 3 mm from the midline and 4 mm anteriorly from the bregma, holes were drilled through the skull bone down to dura mater (without perforation) allowing the placement of two laser-Doppler flow probes to measure CBF. Finally, a 27G blunt canula with side hole was introduced stereotactically 6.5 mm anterior to bregma in the midline at an angle of 30 degrees to the vertical. After 30 minutes of equilibration 250 ul blood was withdrawn from the tail catheter and injected intracranially at a pressure equal to the mean arterial blood pressure (80-100 mmHg). Subsequently the rat was kept under anaesthesia for another 60 minutes to allow recovery from the cerebral insult after which catheters were removed and the incisions closed. The rat was then revitalized and extubated. A subcutaneous injection of carprofen (4.0 mg/kg) (Pfizer, Denmark) was administered and the rat was hydrated subcutaneously using 40 ml isotonic sodium chloride at the end of the operation and at day one. During the period of observation the rat was monitored regularly, and if showing severe distress the animal was prematurely killed. In addition, a series of sham-operated rats were prepared. They went through the same procedure with the exception that no blood was injected intracisternally.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage
View Samples- Mus musculus
- 16 Downloadable Samples
Illumina HiSeq 2500
Description
Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease which is characterized by premature ageing. Affected children show accelerated cardiovascular disease, including atherosclerosis and vascular smooth muscle cell (VSMC) loss, and die at an average age of 14.6 years from myocardial infarction or stroke. The objective of this study was to detect the primary mechanism leading to VSMC death and accelerated atherosclerosis in mouse models of HGPS. In our RNA sequencing experiment we compared transcriptomes of medial aortas from both ubiquitous and VSMC-specific progeric models with its corresponding controls expressing lamin A/C or lamin C only, respectively. Our studies might not only help to find a cure for HGPS but also shed some light on physiological ageing.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Cell line
View Samples- Homo sapiens
- 275 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Tissue samples have been isolated during corornary artery by-pass grafting (CABG)surgery from the atheroscelrotic arterial wall (AAW, aortic root puncture for proxmal ligation of by-pass vessel), non-atherosclertoci arterial wall (NAAW, distal part of mammary artery used a graft for LAD), liver, skeletal muscle (Recturs m), pericardial mediastinal visceral fat) in CAD patients. Carotid lesions samples from 25 validation patients.
Publication Title
Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 32 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gene expression profiles from the aortic arch of Ldlr-/-Apob100/100 Mttpflox/flox Mx1-Cre mice at different stages of atherosclerosis development
Publication Title
Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Illumina HiSeq 2000
Description
No description.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Endothelial cells comprise a key component of the inflammatory response. HUVEC (human umbilical vein endothelial cells) were stimulated with interleukin-1 for 0, 0.5, 1, 2.5 and 6 hours, and analyzed using Affymetrix U133A microarrays, in order to obtain a comprehensive overview of the immediate early to early gene expression profiles. HUVEC were isolated and cultured on gelatine-coated cell culture dishes in M199 medium supplemented with 20% FCS, antibiotics, ECGS (endothelial cell growth supplement) and Heparin as described by Zhang et al., Blood 1996;88:3880-3886. HUVEC were stimulated with 100 U/ml human IL-1 (Biosource) for various periods of time, and total RNA isolated using the RNeasy kit (Qiagen) according to the manufacturer's instructions. Hybridization to one set of human U133A GeneChips (Affymetrix, Santa Clara, CA) and scanning of the arrays was carried out according to manufacturers protocols (https://www.affymetrix.com). Briefly, 5 g of total RNA was used to generate double-stranded cDNA by reverse transcription using a cDNA synthesis kit (Superscript Choice System; Life Technologies, Inc., Rockville, MD) that uses an oligo(dT)24 primer containing a T7 RNA polymerase promoter 3' to the polyT (Geneset, La Jolla, CA), followed by second-strand synthesis. Labeled cRNA was prepared from the double-stranded cDNA by in vitro transcription using T7 RNA polymerase in the presence of biotin-11-CTP and biotin-16-UTP (Enzo, Farmington, NY). The labeled cRNA was purified over RNeasy columns (Qiagen, Valencia, CA). Fifteen g of cRNA was fragmented at 94C for 35 minutes in 40 mmol/L of Tris-acetate, pH 8.1, 100 mmol/L of potassium acetate, and 30 mmol/L of magnesium acetate. The cRNA was then used to prepare 300 l of hybridization cocktail (100 mmol/L MES, 1 mol/L NaCl, 20 mmol/L ethylenediaminetetraacetic acid, 0.01% Tween 20) containing 0.1 mg/ml of herring sperm DNA (Promega, Madison, WI) and 500 g/ml of acetylated bovine serum albumin (Life Technologies, Inc.). Before hybridization, the cocktails were heated to 94C for 5 minutes, equilibrated at 45C for 5 minutes, and then clarified by centrifugation (16,000 x g) at room temperature for 5 minutes. Aliquots of this hybridization cocktail containing 15 g of fragmented cRNA were hybridized to HU133A arrays (Affymetrix, Santa Clara, CA) at 45C for 16 hours in a rotisserie oven at 60 rpm. The arrays were washed using non-stringent buffer (6xSSPE: 0.9 M sodium chloride, 0.06 M sodium phosphate, 6 mM EDTA pH 7.4) at 25C, followed by stringent buffer (100 mmol/L MES, pH 6.7, 0.1 mol/L NaCl, 0.01% Tween 20) at 50C. The arrays were stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR), washed with 6xSSPE, incubated with biotinylated anti-streptavidin IgG, stained again with streptavidin-phycoerythrin, and washed again with 6xSSPE. The arrays were scanned using the GeneArray scanner (Affymetrix). Image analysis was performed with GeneChip software (Affymetrix, MAS 5.0). Normalization was performed by global scaling, with the arrays scaled to an average intensity of 500.
Publication Title
Deciphering regulatory patterns of inflammatory gene expression from interleukin-1-stimulated human endothelial cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 11 Downloadable Samples
- IlluminaHiSeq2500, IlluminaHiSeq2000
Description
The goal of this study is to identify deferentially expressed genes among three groups of individuals of the same family. These groups are : affected, unaffected wild, unaffected carrier.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 5 Downloadable Samples
- Illumina HiSeq 2000
Description
The scientific rationale for the clinical advancement of Lm-based immunotherapies is in part due to hallmark observations in the mouse infection model where a single immunization with sublethal doses of WT Lm confers lifelong protection against lethal WT Lm challenge. Protection is entirely dependent upon potent bacterial-specific CD4+ and CD8+ T cell immunity. While our previous investigations have demonstrated the antitumor potency of therapeutic immunization with LADD-Ag , here we describe for the first time, the immunologic correlates of this antitumor efficacy.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line
View Samples- Triticum aestivum
- 159 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Grain yield and protein content were determined for six wheat cultivars grown over three years at multiple sites and at multiple N-fertilizer inputs. Although grain protein was negatively correlated with yield, some grain samples had higher protein contents than expected based on their yields, a trait referred to as grain protein deviation (GPD). We used novel statistical approaches to calculate GPD across environment and to correlate gene expression in the developing caryopsis with this trait. The yield and protein content were initially adjusted for nitrogen fertilizer inputs, and then adjusted for yield (to remove the negative correlation) resulting in environmental corrected GPD. The transcriptome data for all samples were subjected to Principal Component Analysis (PCA) and ANOVA to identify individual Principal Components (PCs) correlating with GPD alone. Scores of the selected PCs significantly related to cultivar differences and GPD but not to the yield or protein content were identified as reflecting a multivariate pattern of gene expression related to genetic variation in GPD. Sets of genes significant for these PCs and hence GPD were identified as candidate genes determining cultivar differences in GPD.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 53 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
An important but largely unmet challenge in understanding the mechanisms that govern formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from twelve genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasetsbased on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genesprovisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system.
Publication Title
An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes.
Sample Metadata Fields
No sample metadata fields
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