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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

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

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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.

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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

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