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Mus musculus
4 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Target gene of mineralocorticoid receptor (MR) is comparatively unknown, although distal convoluted tubule (DCT) expresses MR in in vivo.
Publication Title
Genome-wide analysis of murine renal distal convoluted tubular cells for the target genes of mineralocorticoid receptor.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
Illumina Genome Analyzer IIx
Description
Purpose: The cholinergic anti-inflammatory pathway (CAP) links the nervous and immune systems and modulates innate and adaptive immunity. The goals of this study are to identify the new downstream signaling of a7nAChR in macrophages. Methods: Peritoneal macrophages isolated from a7nAChR+/+ and a7nAChR-/- mice were treated with nicotine (10 µM) and/or LPS (100 ng/ml), then RNA-seq was performed. Results: Genes were selected that had more than 4-fold relative gene expression in nicotine-treated cells compared to the control group (vehicle-treated). The same calculation was applied to nicotine+LPS-treated cells and LPS-treated cells and 264 genes were identified as genes commonly induced by nicotine based on these two comparisons. Then relative gene expression was compared between a7nAChR+/+- and a7nAChR-/- -derived cells. 18 genes were finally selected whose expressions are suppressed (<1/2) in a7nAChR-/- -derived peritoneal macrophages. Conclusions: Our study represents the first detailed analysis focused on the new downstream signaling of a7nAChR in macrophages, generated by RNA-seq technology. We newly revealed the important anti-inflammatory role of Hes1 in the CAP using some functional experiments. Overall design: Peritoneal macrophage's mRNA profiles of wild type (WT) and a7nAChR-/- mice treated with Nicotine and/or LPS were generated by deep sequencing.
Publication Title
Non-canonical cholinergic anti-inflammatory pathway-mediated activation of peritoneal macrophages induces Hes1 and blocks ischemia/reperfusion injury in the kidney.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Many neural progenitor cells present in the fetus, but also in adult brain, which play a major role for the reproduction for healingin regeneration of neuronal cells, when differentiated cells are damaged. However, effects of radiation effect on undifferentiated neural progenitor cells remained unclear. The radiation doses of medical exposure, pollution by nuclear power plant accidents, and other exposure of workers; medical workers, airline crews, and astronaut have been focused. In this study, we report the effects of low- to middle- dose doses of radiation on cultured human neural progenitor cells (hNPC) differentiated derived from embryonic stem (ES) cells, which are partially compared with those of human umbilical vein endothelial cell (HUVEC).
Publication Title
Effects of Chronic Low-Dose Radiation on Human Neural Progenitor Cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Oryza sativa
- 24 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g; flowering and floral organ identity), in stress-related developmental processes such as abscission, fruit ripening and senescence and the role of some of them in stress response regulation was reported. The aim of this study was to decipher the genes that are under the control of the OsMADS26 transcription factor in rice in standard or osmotic stress condition.
Publication Title
OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Total 23 samples were derived from [1] HUVEC treated in the absence (0h) or presence of hypoxia (1, 2, 4, 8, 12, and 24 hrs) to determine hypoxia-regulated gene in endothelial cells, [2] control siRNA or HIF1 siRNA transfected HUVEC cells treated in the absence or presence of hypoxia, [3] control siRNA or KDM3A siRNA transfected HUVEC cells treated in the absence or presence of hypoxia, [4] ChIP-seq data for HIF1 binding sites and histone modifications under normoxia and hypoxia in endothelial cells.
Publication Title
Dynamic change of chromatin conformation in response to hypoxia enhances the expression of GLUT3 (SLC2A3) by cooperative interaction of hypoxia-inducible factor 1 and KDM3A.
Sample Metadata Fields
Cell line, Treatment
View Samples
GSE46054- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
In order to clarify the downstream target genes of SPAG4, we performed knockdown of SPAG4 using siRNA both under normoxia and hypoxia.
Publication Title
Sperm-associated antigen 4, a novel hypoxia-inducible factor 1 target, regulates cytokinesis, and its expression correlates with the prognosis of renal cell carcinoma.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
Bulk RNA sequencing data from neural progenitor cells under conditions of low or high growth factor and Notch pathway activation Overall design: Cells were treated with high (20 ng/ml EGF and FGF) or low (0.5 ng/ml EGF) recombinant growth factors, with or without Notch pathway inhibitor (DAPT, 10 uM) for 12h.
Publication Title
<i>Cis-</i>activation in the Notch signaling pathway.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 44 Downloadable Samples
- Illumina HiSeq 2000
Description
The complete transcriptomes of kidney cortex from 3 ?-HIF2aM3 18 month old TG+ male mice and 3 age matched wild type (WT) C57BL/6 male mice were sequenced on an Illumina HiSeq2000 Sequencer. Overall design: Examination of complete transcriptome of kidney cortex between ?-HIF2aM3 TG+ male mice and wild type C57BL/6 male mice
Publication Title
Activation of HIF2α in kidney proximal tubule cells causes abnormal glycogen deposition but not tumorigenesis.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Rattus norvegicus
- 5 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Alterations in the composition of the gut microbiome have an emerging role in brain function and behaviour. We have porposed that short chain fatty acids (SCFA) including propionate and butyrate which are present in the diet and are fermantation products of many gastrointestinal bacteria are contributing environmental factors in autism spectrum disorders (ASD). Here we used the microarray technology to compare global changes in gene expression profiles following exposure of PC12 cells to structurally related SCFA propionate and butyrate each in two different concentrations. Large number of affected genes, common for both SCFA were identified, including genetic networks and GO processes implicated in ASD.
Publication Title
Enteric bacterial metabolites propionic and butyric acid modulate gene expression, including CREB-dependent catecholaminergic neurotransmission, in PC12 cells--possible relevance to autism spectrum disorders.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 26 Downloadable Samples
- Illumina HiSeq 2000
Description
Lysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are mostly linked to gene repression. However, functions of repressive histone methylation dynamics during inflammatory responses remain poorly understood. Here, we show that lysine demethylase 7A (KDM7A) and 6A (UTX) are rapidly transported to nuclear factor kappa-B (NF-?B) related elements in human endothelial cells in response to tumor necrosis factor (TNF)-a. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and cooperatively activate NF-?B dependent inflammatory genes. Furthermore, using both in situ Hi-C and other 3C based technology, loops between super enhancers (SEs) are newly formed following TNF-a-stimuli at NF-?B-dependent inflammatory loci where KDM7A- and UTX-recruitment coincide. Collectively, these findings suggest that erasing of repressive histone marks by KDM7A and UTX within NF-?B-related elements might functionally associate with formation of SE-SE three-dimensional interactions and could be a cue signal during inflammatory responses in human endothelial cells. Overall design: Total 29 samples were derived from [1] HUVECs in the absence or presence of TNF-alpha (0, 4, and 24 hrs) to determine TNF-alpha-responsive genes during inflammation, [2] si control, siKDM7A, siUTX, or siKDM7A+siUTX transfected HUVECs under TNF-alpha-stimuli (4 hrs) to understand molecular function of KDM7A and UTX during inflammation.
Publication Title
Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells.
Sample Metadata Fields
Subject, Time
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