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GSE19089
Homo sapiens
6 Downloadable Samples
Illumina HumanHT-12 V3.0 expression beadchip
Description
Analysis of gene expression levels from oral tumor and normal tissue. The purpose of this experiment was to compare profiles of gene expression between tumor and negative margin tissue from matched patient samples.
Publication Title
Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Effects of treatment with Nimodipine on N9 cells
Publication Title
Nimodipine fosters remyelination in a mouse model of multiple sclerosis and induces microglia-specific apoptosis.
Sample Metadata Fields
Treatment
View Samples- Bos taurus
- 23 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
This study provides the first comprehensive analysis of gene expression and transcriptome dynamics of bovine metaphase II oocytes and in vivo developing bovine embryos.
Publication Title
Genome-wide expression profiling reveals distinct clusters of transcriptional regulation during bovine preimplantation development in vivo.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Besides symptoms caused by central nervous system (CNS) lesions, the majority of patients with multiple sclerosis (MS) also exhibit gastrointestinal dysfunction that has frequently been noted, but was not directly linked to the autoimmune etiology of the disease.We studied the enteric nervous system (ENS) in a murine model of MS by histology and electron microscopy. Serum IgG against enteric neurons and enteroglia was measured by ELISA and binding to the ENS was confirmed by immunohistochemistry. Target antigens were identified by mass spectrometry. Gastrointestinal dysfunction was determined by measuring dye transit time. RNA expression profiling was conducted with small intestines of MP4-immunized and control-immunized mice. Data from the mouse model were confirmed in MS patients by immunohistochemistry of the ENS in bowel resectates. In addition, ELISA was performed on plasma samples to detect antibodies against four specific target antigens as identified in the mouse model. ENS degeneration was evident already before the onset of clinical disease in the mouse model. Pathology was predominantly antibody-mediated and caused a significant decrease in gastrointestinal transit, which was associated with severe gliosis of the ENS. Unlike the dense infiltrates that developed in the perivascular compartments of the CNS of MP4-immunized mice, the infiltrates in the ENS consisted of single cells scattered throughout the tissue. RNA expression profiling could support these results, as the expression of inflammatory markers in the small intestine was similar between MP4-immunized and HEL-immunized mice. We identified four specific target antigens derived from enteric neurons and/or enteroglia. Antibodies against all four target antigens were present in MS patients. MS patients also showed gliosis and signs of ENS degeneration in the small intestine. For the first time, this study establishes a pathomechanistic link between the well-established autoimmune attack on the CNS and the ENS in MS. The presence of ENS pathology prior to CNS degeneration introduces entirely novel ways to explain MS etiology and immunopathogenesis.
Publication Title
The enteric nervous system is a potential autoimmune target in multiple sclerosis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
Illumina Genome Analyzer IIx
Description
High-throughput sequencing of mRNA from mouse lung infected with 1918 pandemic influenza virus revealed that reactive oxygen species scavenger EUK-207 treatment resulted in decreased expression of inflammatory response genes and increased lung metabolic and repair responses.
Publication Title
Treatment with the reactive oxygen species scavenger EUK-207 reduces lung damage and increases survival during 1918 influenza virus infection in mice.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 120 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Gene expression analysis has been established as a tool for the characterization of genotoxic mechanisms of chemical mutagens. This approach has been shown to differentiate between DNA reactive genotoxins and non-DNA reactive or indirectly-acting genotoxins. In this context, it has been suggested that expression analysis is capable of distinguishing compounds that cause DNA damage from those that interfere with mitotic spindle function. Formaldehyde (FA) is known to be a DNA-reactive substance which mainly induces chromosomal damage in cultured mammalian cells. However, there has been concern that FA might also act as an aneugen (i.e., induce aneuploidy) but recent cytogenetic studies did not support this assumption. To further characterize FA's genotoxic mode of action, we now used gene expression profiling as a molecular tool to differentiate between clastogenic and aneugenic activity. TK6 cells were exposed to FA for 4 and 24 h and changes in gene expression were analyzed using a whole-genome human microarray. Results were compared to the expression profiles of two DNA-damaging clastogens (methyl methanesulfonate [MMS] and ethyl methanesulfonate [EMS]) and two aneugens (colcemid [COL] and vincristine [VCR]). The gene expression profiles indicated that clastogens and aneugens induce discriminable gene expression patterns. The expression profile of FA showed more similarities to clastogens than to aneugens. Hierarchical clustering analysis as well as several class prediction algorithms revealed a much closer relationship of FA with clastogens than with aneugens. A pathway analysis of differentially regulated genes also demonstrated an overall better agreement of FA with clastogens than with aneugens. Altogether, the results of this study revealed great similarities in gene expression in response to FA and clastogens but did not support an aneugenic activity of FA.
Publication Title
Characterization of formaldehyde's genotoxic mode of action by gene expression analysis in TK6 cells.
Sample Metadata Fields
Cell line, Treatment
View Samples- Bos taurus
- 16 Downloadable Samples
- Bovine Gene 1.1 ST Array (bovgene11st)
Description
Steer liver transcriptome
Publication Title
Differential expression of genes related to gain and intake in the liver of beef cattle.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Mutations involving the NFKB pathway are present in at least 17% of multiple myeloma (MM) tumors and 40% of MM cell lines (MMCL). These mutations, which are thought to be progression events, enable MM tumors to become less dependent on extrinsic bone marrow signals that activate NFKB. Studies on a panel of 50 MMCL provide some clarification of the mechanisms through which these mutations act and the significance of classical vs alternative activation of NFKB. First, only one mutation (NFKB2) selectively activates the alternative pathway, whereas several mutations (CYLD, NFKB1, TACI) selectively activate the classical pathway. However, most mutations affecting NIK level (NIK, TRAF2, TRAF3, cIAP1&2, CD40) activate the alternative but often both pathways. Second, we confirm the critical role of TRAF2 in regulating NIK degradation, whereas TRAF3 enhances but is not essential for cIAP1/2-mediated proteosomal degradation of NIK in MM.
Publication Title
Classical and/or alternative NF-kappaB pathway activation in multiple myeloma.
Sample Metadata Fields
Cell line
View Samples- Bos taurus
- 16 Downloadable Samples
- Bovine Gene 1.1 ST Array (bovgene11st)
Description
Steer spleen transcriptome
Publication Title
Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake.
Sample Metadata Fields
Specimen part
View Samples- Danio rerio
- 6 Downloadable Samples
- IlluminaHiSeq2500, IlluminaHiSeq4000
Description
Epithelial cell adhesion molecule EpCAM is a transmembrane glycoprotein that is dynamically expressed in human and murine renal epithelia during development. The levels of EpCAM in the renal epithelium are upregulated both during regeneration after ischemia/reperfusion injury and in renal-derived carcinomas. The role of EpCAM in early kidney development, however, has remained unclear. To identify potential programs and signaling pathways that are controlled by EpCAM during pronephros development, we developed a method to study the transcriptomes of specific pronephric segments. Combining laser capture microdissection (LCM) with RNA sequencing (RNA-seq), we generated genome-wide transcriptional profiles of the distal late tubules of wild type and EpCAM-deficient embryos. Overall design: RNA-seq of LCM-dissected pronephric cells from EpCAM-deficient and control zebrafish embryos
Publication Title
EpCAM controls morphogenetic programs during zebrafish pronephros development.
Sample Metadata Fields
No sample metadata fields
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