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Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [Affymetrix]

ABSTRACT: The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed into cDNAs and categorized in 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days We then used Affymetrix microarray platform to profile the gene expression of the 3 HT29 cell groups (3 replicates in each group) in order to search for differentially expressed genes

ORGANISM(S): Homo sapiens

PROVIDER: GSE41364 | GEO | 2013/09/17

SECONDARY ACCESSION(S): PRJNA176692

REPOSITORIES: GEO

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Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [RNA-Seq]

Project description:The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed to build cDNA libraries and categorized into 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days. This experiment was also performed parallel on a commercial Affymetrix microarray [GSE41364] and the aim of the study was to compare the two platforms on gene expression measurements and differentially expressed gene (DEG) detection. The results showed a strong correlation between the two platforms, yet it also confirmed the existence of fixed and proportional biases on the gene expression measurements between microarray and RNA-Seq. The DEG analysis indicated the relative superiority of DESeq method in terms of its performance; high consistency was confirmed between DESeq, baySeq methods from RNA-Seq and SAM/eBayes from microarray data. Experiment on human colon cancer HT29 cell line treated with 3 concentrations of 5-aza-deoxy-cytidine

2013-09-17 | E-GEOD-41586 | biostudies-arrayexpress

Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [RNA-Seq]

2013-09-17 | GSE41586 | GEO

Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [Affymetrix]

Project description:The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed into cDNAs and categorized in 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 Î¼M 5-Aza); 2) 5Î¼M 5-Aza and 3) 10 Î¼M 5-Aza; for five days We then used Affymetrix microarray platform to profile the gene expression of the 3 HT29 cell groups (3 replicates in each group) in order to search for differentially expressed genes The transcriptional response of HT-29 (ATCC) colon cancer cell line under 3 concentrations of 5-aza-deoxy-cytidine was investigated based on their RNA expression profiles

2013-09-17 | E-GEOD-41364 | biostudies-arrayexpress

Expression data for HT29 cells treated with 5-aza-deoxy-cytidine

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-09-17 | GSE41588 | GEO

Expression data for HT29 cells treated with 5-aza-deoxy-cytidine

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-09-17 | E-GEOD-41588 | biostudies-arrayexpress

Modulation of immunomodulatory peptide activity by 2-deoxy-d-glucose

Project description:The goal of this study was to identify the role of glycolysis in the activity of immunomodulatory peptides with respect to macrophage function using the glycolytic inhibitor 2-deoxy-d-glucose

2016-10-29 | GSE74508 | GEO

Gene expression of SKOV3 cells after no treatment or treatment with 50 microM peracetylated GlcNAc or peracetylated 4-deoxy-GlcNAc for three days

Project description:Heparan sulfate (HS), a long linear polysaccharide, is implicated in various steps of tumorigenesis, including angiogenesis. We successfully interfered with HS biosynthesis using a peracetylated 4-deoxy analog of the HS constituent GlcNAc and studied the compound’s metabolic fate and its effect on angiogenesis. The 4-deoxy analog was activated intracellularly into UDP-4-deoxy-GlcNAc and HS expression was inhibited up to ~96% (IC50 = 16 µM). HS chain size was reduced, without detectable incorporation of the 4-deoxy analog, likely due to reduced levels of UDP-GlcNAc and/or inhibition of glycosyltransferase activity. Comprehensive gene expression analysis revealed reduced expression of genes regulated by HS binding growth factors as FGF-2 and VEGF. Cellular binding and signaling of these angiogenic factors was inhibited. Micro-injection in zebrafish embryos strongly reduced HS biosynthesis, and angiogenesis was inhibited in both zebrafish and chicken model systems. All these data identify 4-deoxy-GlcNAc as a potent inhibitor of HS synthesis which hampers pro-angiogenic signaling and neo-vessel formation.

2013-08-23 | GSE48284 | GEO

Human scrotum and labia majora samples treated with DHT and/or AZA

Project description:Human scrotum and labia majora samples treated with DHT and/or AZA A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed. Compound Based Treatment: dihydrotestosterone (DHT), 5-aza-deoxy-cytidine (AZA), none or both Cell Line: normal scrotum or labia majora derived from complete androgen insensitivity syndrome due to inactivating mutation of the androgen receptor gene

2009-05-20 | GSE11847 | GEO

Deep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence of 2-deoxy-D-glucose (DOG) at 4 different time points

Project description:Background: C. elegans fed with a chemical inhibitor of glucose, namely 2-deoxy-D-glucose (DOG), exhibit considerably extended life span. DOG, in contradiction to D-glucose, cannot be metabolized in the glycolytic pathway. This results in the fact that less glucose is available for ATP production, and thus makes DOG-feeding of the roundworms equivalent to glucose restriction. The RNA-seq data comprises 4 age groups (1, 5, 10 and 20 days after L4) Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

2013-11-06 | GSE46344 | GEO

Transcriptomics profile of polyQ expressing U2OS cells and clofazimine treated polyQ expressing U2OS cells

Project description:To better understand the mechanism by which CFZ impacts polyQ toxicity, we conducted a transcriptomic analysis in polyQ94-EGFP expressing U2OS (5μM, 8 days). Data from a transcriptomics experiment in polyQ94-U2OS cells treated with CFZ (5 μM, 8day) was compared to a DMSO-treated control.

2023-05-11 | GSE222758 | GEO

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