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GSE2336
Mus musculus
24 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Goal of experiment: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference). Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice. Preparation of cDNA. Double-stranded cDNA was synthesized from purified RNA. The first strand was synthesized by incubating 5 g of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3 Genset Corp, San Diego, CA) at 70C for 10 minutes. Samples were incubated for 1 hour at 42C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 M each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 l. Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16C: 1X second strand reaction buffer, 200 M dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 l with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen). A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated. Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA. The following mix was incubated at 37C for 5 hours: 1 g of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase. Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts. Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94C. (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc). After fragmentation, the samples were stored at -20C until the hybridization was performed. Sample hybridization. Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice. For each array,15 g of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen), 0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 l). Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99C and then 45C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45C with rotation. After incubation, the buffer solution was removed from the array. The array was filled with 300 l of the hybridization cocktail, placed in a rotisserie box in a 45C oven, and incubated for 16 hours while rotating at 60 rpm. Washing and staining of array. The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25C, 4 cycles of 15 mixes/cycle with wash buffer B at 50C, 30 minute incubation with staining solution at 25C, 10 cycles of 4 mixes/cycle with wash buffer A at 25C. Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20). (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker). Wash buffer B stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20). Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 g/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 l). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]). Analysis. After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix). Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.
Publication Title
Identification of candidate genes that influence sex hormone-dependent disease phenotypes in mouse lupus.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
MB114 cells cultured on Matrigel for 1, 5, 15, 25 hours
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit a large difference in a number of alcohol and drug related behaviors. This study examined the expression levels of transcripts in these strains in the cerebellum, which is a major target of ethanols actions in the CNS, in order to find differentially expressed candidate genes for these phenotypes. Cerebellum was specifically chosen due to the fact that Purkinje cell sensitivity to ethanol in these strains is highly correlated to "sleep time", the measure of ethanol sensitivity used with these strains. Naive mice were used because differences in sensitivity are observed upon initial exposure to ethanol.
Publication Title
Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 193 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
PAPER 1:"Identification of novel subgroups of high-risk pediatric precursor B acute lymphoblastic leukemia (B-ALL) by unsupervised microarray analysis: clinical correlates and therapeutic implications. A Children's Oncology Group (COG) study."
Publication Title
Gene expression classifiers for relapse-free survival and minimal residual disease improve risk classification and outcome prediction in pediatric B-precursor acute lymphoblastic leukemia.
Sample Metadata Fields
Sex, Specimen part, Race
View Samples- Mus musculus
- 23 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Equine herpesvirus 1 (EHV-1) is a major pathogen affecting equines worldwide and causes respiratory disease, abortion, and in some cases, neurological disease.EHV-1strain KyA is attenuated in the mouse and equine, whereaswild-typestrain RacL11 induces severe inflammatory infiltration of the lung, causing infected mice to succumb at 4 to 6 days post-infection. Our previous results showed that EHV-1 KyA immunization protected CBA mice from pathogenic RacL11 challenge at 2 and 4 weeks post-immunization, and that the infection with theattenuatedKyA elicits protective humoral and cell-mediated immune responses.To investigate the protective mechanisms of EHV-1 KyA by innate immune responses, CBA mice immunized with live KyA were challenged with RacL11 at various timespost-vaccination. KyA immunization effectively protected CBA mice from RacL11 challenge at 1 to 7 dayspost-immunization. Immunized mice lost less than 10% of their preinfection body weight and rapidly regained body weight. Lung virus titers in EHV-1 KyA-immunized CBA mice were 1,000-fold lower at 2 days post-RacL11 challenge than lungs of non-immunized mice, which was indicative of accelerated virus clearance. Affymetrix microarray analysis revealed thatIFN-and16 antiviral interferon-stimulated genes (ISGs) were upregulated 3.1- to 48.2-fold at 8 h post-challengein the lungs of RacL11-challenged mice that had been immunized with KyA. Murine IFN-inhibitedEHV-1 infection of murine alveolar macrophage MH-S cells andeffectively protected mice against lethal EHV-1 challenge, suggesting that IFN-expression may be important in mediating protection elicited by KyA immunization. These results suggestthat EHV-1 KyA can be used asa live attenuated EHV-1 vaccine as well as a prophylactic agent in horses.
Publication Title
Immunization with Attenuated Equine Herpesvirus 1 Strain KyA Induces Innate Immune Responses That Protect Mice from Lethal Challenge.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Acquired imatinib resistance in chronic myelogenous leukemia (CML) can be the consequence of mutations in the kinase domain of BCR-ABL or increased protein levels. However, as in other malignancies, acquired resistance to cytostatic drugs is a common reason for treatment failure or disease progression. As a model for drug resistance, we developed a CML cell line resistant to cyclophosphamide (CP). Using oligonucleotide arrays, we examined changes in global gene expression. Selected genes were also examined by real-time PCR and flow cytometry. Neither the parent nor the resistant lines had mutations in their ATP binding domain. Filtering genes with a low-base line expression, a total of 239 genes showed significant changes (162 up- and 77 down-regulated) in the resistant clone. Most of the up-regulated genes were associated with metabolism, signal transduction, or encoded enzymes. The gene for aldehyde dehydrogenase 1 was over-expressed more than 2000 fold in the resistant clone. BCR-ABL was expressed in both cell lines to a comparable extent. When exposed to the tyrosine kinase inhibitors imatinib and nilotinib, both lines were sensitive. In conclusion, we found multiple genetic changes in a CML cell line resistant to CP related to metabolism, signal transduction or apoptosis. Despite these changes, the resistant cells retained sensitivity to tyrosine kinase inhibitors.
Publication Title
Comparative gene expression analysis of a chronic myelogenous leukemia cell line resistant to cyclophosphamide using oligonucleotide arrays and response to tyrosine kinase inhibitors.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 65 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The respiratory system is a complex network of many cell types, including subsets of macrophages and dendritic cels, that work together to maintain steady-state respiration. Due to limitations in acquiring cells from healthy human lung, these subsets remain poorly characterized transcriptionally and phenotypically. We set out to systemically identify these subsets in human airways, by developing a schema of isolating large numbers of cells by whole lung bronchoalveolar lavage. Six subsets of phagocytic antigen presenting cells were consistently observed, which varied in their ability to internalize bacterial particles. Subsets could be further separated by their inherent capacities to upregulate CD83, CD86, and CCR7. Whole genome transcriptional profiling revealed a clade of true dendritic cells distinct from a macrophage/monocyte clade. Each clade, and each member of both clades, could be discerned by specific genes of increased expression, which would serve as markers for future studies in healthy and diseased states.
Publication Title
Transcriptional Classification and Functional Characterization of Human Airway Macrophage and Dendritic Cell Subsets.
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 26 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The aim of this study was to investigate the association of gene expression profiles in subcutaneous adipose tissue with percent of total body weight change in 26 kidney transplant recipients.
Publication Title
Expression levels of obesity-related genes are associated with weight change in kidney transplant recipients.
Sample Metadata Fields
Sex, Race
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The overall goal of this project is to investigate the role of TGF-beta signaling in epithelial cells as it pertains to the orientation of muscle fibers in the soft palate during embryogenesis. Here, we first conducted gene expression profiling of the anterior and posterior portions of the palate from wild-type mice. In addition, we also conducted gene expression profiling of the posterior palate in mutant mice with an epithelium-specific conditional inactivation of the Tgfbr2 gene. The latter mice provide a model of submucosal cleft palate, which is a congenital birth defect commonly observed in many syndromic conditions.
Publication Title
TGFβ regulates epithelial-mesenchymal interactions through WNT signaling activity to control muscle development in the soft palate.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The overall goal of this project is to investigate the role of Erk2-mediated signaling in regulating the cellular metabolism of cranial neural crest (CNC) cells during palate development. Here, we conducted gene expression profiling of palate tissue from wild type mice as well as those with a neural crest specific conditional inactivation of the Erk2 gene. The latter mice exhibit micrognathia, tongue defects and cleft palate, which is among the most common congenital birth defects and observed in many syndromic conditions.
Publication Title
Disruption of the ERK/MAPK pathway in neural crest cells as a potential cause of Pierre Robin sequence.
Sample Metadata Fields
Sex, Specimen part
View Samples