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Mus musculus
6 Downloadable Samples
Affymetrix Mouse Clariom S Array (clariomsmouse)
Description
To assess the role of the aryl hydrocarbon receptor (AHR) receptor in dendritic epidermal T cells (DETC), we sorted DETC from 2 weeks old mice homozygous and heterozygous for AHR-knockout. While DETC are not maintained in the epidermis of mice with a homozygous AHR-knockout, those in heterozygous mice devellop normally. The age at 2 weeks is critical for the DETC establishment and the peak time of the so-called proliferation burst of DETC in wildtype mice. DETC were identified in epidermal cell suspension by expression of the gamma-delta T cell receptor. The DETC proportion of live epidermal cells was between 10-15 % in Ahr-het and 2-4 % in Ahr-ko mice. After FACS-sorting to a purity of 90-98 %, DETC were lysed and their RNA was extracted. Three RNA samples for each genotype were generated, by pooling the RNA of 2-3 mice for each sample. RNA was processed and hybridized to Applied BiosystemsTM ClariomTM S Mouse Gene Expression Microarrays. Using the Software package R the data were normalized using the Robust Multichip Average algorithm (RMA) and significance of differentially regulated genes was assessed by the False Discovery Rate (FDR) using the Benjamini and Hochberg’s method.
Publication Title
The small chain fatty acid butyrate antagonizes the TCR-stimulation-induced metabolic shift in murine epidermal gamma delta T cells.
Sample Metadata Fields
Age, Specimen part
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GSE63875- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We analyzed miRNA profiles in normal liver and identified miR-709, a highly abundant miRNA in this tissue. Through microarray analysis, gene targets were identified. Thirty-six genes were significantly down-regulated >2-fold in the miR-709-treated relative to the control group, and at least three of them, including Ras-related protein 11b (Rab11b), phosphatidylcholine transfer protein (Pctp), and carboxylesterase 1g (Ces1g), are direct targets. miR-709 regulates genes implicated in cytoskeleton organization, extracellular matrix attachment, cell proliferation and fatty acid metabolism, suggesting a coordinated response during cell division, when cytoskeleton remodeling requires substantial changes in gene expression.
Publication Title
Gene targets of mouse miR-709: regulation of distinct pools.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Hematopoietic stem cells (HSC) continuously regenerate a complete hematologic and immune system. Very few genes that regulate this process have yet been identified. In order to identify factors governing differentiation, we have compared the transcriptome of highly purified HSC with their differentiated progeny, including erythrocytes, granulocytes, monocytes, NK cells, activated and nave T-cells, and B-cells. Chromosomal analysis revealed that HSC were more transcriptionally active than other cell types across most chromosomes. Each lineage expressed ~100 to 400 genes uniquely, including many previously uncharacterized genes. Overexpression of two fingerprint genes resulted in a significant bias in differentiation indicating a role in cell fate determination, demonstrating the utility of these data for modulation of specific cell types.
Publication Title
Hematopoietic fingerprints: an expression database of stem cells and their progeny.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 6 Downloadable Samples
IlluminaGenomeAnalyzerII, IlluminaHiSeq2000
Description
The Gata4 transcription factor is essential for normal heart development, but the molecular basis for its function remain poorly understood. We profiled at the whole genome level transcript changes in cardiomyocytes when Gata4 is depleted from zebrafish embryos. Our objective was to elucidate the cardiomyocyte-specific molecular program functioning downstream of Gata4 in order to better understand the role of Gata4 in cardiac morphogenesis. Overall design: Six samples in total are deposited. Three replicate control samples and three replicate Gata4 morphant samples were analyzed.
Publication Title
Small heat shock proteins Hspb7 and Hspb12 regulate early steps of cardiac morphogenesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
To better understand the differentiation and survival defect of Nrf2-/- HSPC, we performed gene expression studies on KSL cells isolated by FACS from Nrf2+/+ and Nrf2-/- mice.
Publication Title
The redox-sensitive transcription factor Nrf2 regulates murine hematopoietic stem cell survival independently of ROS levels.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Epithelial Hedgehog (Hh) ligands regulate several aspects of fetal intestinal organogenesis and emerging data implicate the Hh pathway in inflammatory signaling in adult colon. We investigated the effects of chronic Hh inhibition in vivo and profiled molecular pathways acutely modulated by Hh signaling in the intestinal mesenchyme.
Publication Title
Hedgehog is an anti-inflammatory epithelial signal for the intestinal lamina propria.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The E-protein transcription factors E2A and HEB play important roles at several stages of hematopoiesis. However, the exact mechanism for theire action and the main targets in the LY6D negative common lymphoid progentior (CLP) compartment remains unknown. By adressing this question, we will gain important infromation regarding the early events leading to B-cell specification.
Publication Title
The transcription factors E2A and HEB act in concert to induce the expression of FOXO1 in the common lymphoid progenitor.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Aberrant activation of FGFR3 via overexpression or mutation is a frequent feature of bladder cancer; however, its molecular and cellular consequences and functional relevance to carcinogenesis are not well understood. In this study with a bladder carcinoma cell line expressing inducible FGFR3 shRNAs, we sought to identiy transcriptional targets of FGFR3 and investigate their contribution to bladder cancer development.
Publication Title
FGFR3 stimulates stearoyl CoA desaturase 1 activity to promote bladder tumor growth.
Sample Metadata Fields
Cell line
View Samples GSE1559- Mus musculus
- 16 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
HSC (Sca+ SP) were isolated from 8-12 week C57B6 mice at various time points after treatment with 5-Fluorouracil. RNA was isolated from 50,000-100,000 FACS sorted cells and subjected to two rounds of T7 based linear amplification using Ambion's Message Amp kit. Two replicates from each time point were analyzed.
Publication Title
Molecular signatures of proliferation and quiescence in hematopoietic stem cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 48 Downloadable Samples
- Affymetrix HT Human Genome U133A Array (hthgu133a)
Description
Molecular distinctions between the stasis and telomere attrition senescence barriers in cultured human mammary epithelial cells
Publication Title
Molecular distinctions between stasis and telomere attrition senescence barriers shown by long-term culture of normal human mammary epithelial cells.
Sample Metadata Fields
Specimen part, Subject
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