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Expression data from E18 mouse dorsal telencephalon

ABSTRACT: Neurons deficient in both GSK-3 alpha and beta isoforms fail to migrate properly and develop abnormal morphology. In exploring mechanisms, we found no change in Wnt transcriptional target genes. Verified decrease in GSK-3B exon 2 RNA was extracted from presumptive somatosensory cortices of E18 GSK-3 alpha -/- beta loxp/loxp (control) and GSK-3:Nex conditional mutant embryos. There were totally 6 samples: 3 control and 3 mutants.

ORGANISM(S): Mus musculus

SUBMITTER: William Snider

PROVIDER: E-GEOD-58727 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from E18 mouse dorsal telencephalon

Project description:Neurons deficient in both GSK-3 alpha and beta isoforms fail to migrate properly and develop abnormal morphology. In exploring mechanisms, we found no change in Wnt transcriptional target genes. Verified decrease in GSK-3B exon 2

2014-07-29 | GSE58727 | GEO

Identifying mRNA targets of microRNA in clear cell renal cell carcinoma

Project description:A bioinformatic approach to identify targets of microRNA in cancer. Keywords: Patient sample study Samples GSM413237-GSM413270: Total RNA from 17 RCC tumors and 17 corresponding non-tumor samples was hybridized against a common reference RNA (Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature 2000;406:747-752) for gene expression analysis. Samples GSM413271-GSM413304: MicroRNA from 17 RCC tumors and 17 corresponding non-tumor samples were hybridized on a single channel platform for miRNA expression analysis.

2011-02-28 | E-GEOD-16441 | biostudies-arrayexpress

Translation State Array Assay for C elegans IFE-1-dependent mRNAs

Project description:Relative polysomal loading changes for wild type (N2) versus ife-1(bn127) C. elegans strains Strain ife-1(bn127) is null for the gene encoding one of five eIF4E isoforms in the worm, IFE-1. Only this isoform associates with P granules. Resolution of translating and non-translating mRNAs from WT and mutant worms on 10-45% sucrose gradients. Comparision was by ratios of polysomal content. Please note that each sample data table contains raw signal directly imported from the Affymetrix files and the ratio of signals, P/(NP+P), and fold-changes were further calculated. The TSAA_overview.xls contains more datails about the TSAA procedure and 'complete_data.xlsx' contains complete TSAA data output.

2016-01-07 | E-GEOD-74459 | biostudies-arrayexpress

Expression data from P15 mouse testes control and Ikbkap-knockout mice

Project description:Ikbkap/Elp1 regulates genes involved in spermatogenesis. Ikbkap deficiency causes male infertility by disrupting meiotic progression. In this dataset, we include the expression data for control and Ikbkap-knockout mouse testis. We analyzed the gene expression in control and Ikbkap-knockout testes using the the Affymetrix MoGene-1_0-st-v1 platform. Three replicates per genotype.

2013-12-31 | E-GEOD-42230 | biostudies-arrayexpress

Gene expression of TCR-alpha/beta CD4- CD8- human T cells

Project description:The origin and function of human double negative (DN) TCR-alpha/beta T cells is unknown. They are thought to contribute to the pathogenesis of systemic lupus erythematosus because they expand and accumulate in inflamed organs. Here we provide evidence that human TCR-alpha/beta CD4- CD8- DN T cells derive exclusively from activated CD8+ T cells. Freshly isolated TCR-alpha/beta DN T cells display a distinct gene expression and cytokine production profile. DN cells isolated from peripheral blood as well as DN cells derived in vitro from CD8+ T cells, produce a defined array of pro-inflammatory mediators that includes IL-1, IL-17, IFN-gama, CXCL3, and CXCL2. These results indicate that, upon activation, CD8+ T cells have the capacity to acquire a distinct phenotype that grants them inflammatory capacity. TCR-alpha-beta+ CD25- T cells from healthy human individuals were sorted into CD4+, CD8+, and CD4-CD8- T cells. Cell lysis and RNA extraction was performed immediately. RNA from each cell subset was pooled.

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Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [Expression]

Project description:Ten-eleven translocation (Tet) family of DNA dioxygenases converts 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5- carboxylcytosine (5caC) through iterative oxidation reactions. While 5mC and 5hmC are relatively abundant, 5fC and 5caC are at very low levels in the mammalian genome. Thymine DNA glycosylase (TDG) and base excision repair (BER) pathways can actively remove 5fC/5caC to regenerate unmethylated cytosine, but it is unclear to what extent and at which part of the genome such active demethylation processes take place. Here, we have performed high-throughput sequencing analysis of 5mC/5hmC/5fC/5caC- enriched DNA using modification-specific antibodies and generated genome-wide distribution maps of these cytosine modifications in wild-type and Tdg-deficient mouse embryonic stem cells (ESCs). We observe that the steady state 5fC and 5caC are preferentially detected at repetitive sequences in wild-type mouse ESCs. Depletion of TDG causes marked accumulation of 5fC and 5caC at a large number of distal gene regulatory elements and transcriptionally repressed/poised gene promoters, suggesting that Tet/TDG-dependent dynamic cycling of 5mC oxidation states may be involved in regulating the function of these regions. Thus, comprehensive mapping of 5mC oxidation and BER pathway activity in the mammalian genome provides a promising approach for better understanding of biological roles of DNA methylation and demethylation dynamics in development and diseases. Gene expression comparison of control and Tdg knockdown mouse embryonic stem cells.

2013-04-18 | E-GEOD-46112 | biostudies-arrayexpress

Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics

2013-04-18 | E-GEOD-42250 | biostudies-arrayexpress

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2011-11-05 | E-GEOD-33093 | biostudies-arrayexpress

Wnt/β-catenin signaling activation induces differentiation in human limbal epithelial stem cells cultured ex vivo

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Gene expression profiles elicited by estradiol and endoxifen in MCF7 parental and ER-beta expressing breast cancer cells

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2011-02-18 | E-GEOD-27375 | biostudies-arrayexpress

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