Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE41586 | GEO | 2013/09/17

SECONDARY ACCESSION(S): PRJNA177604

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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 [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 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

2013-09-17 | GSE41364 | 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

Study for evaluating the effect of different microarray platforms on gene expression measurements

Project description:Study for evaluating the effect of different microarray platforms on gene expression measurements

| PRJNA531720 | ENA

Deglycosylated azithromycin targets transgelin to enhance intestinal smooth muscle function

Project description:Human intestinal smooth muscle cells (HISMCs) were collected from Deg-AZM-treated (20 μM, 24h) and control groups. Cells were incubated with Trizol (1 mL) at room temperature for 15 min. Microarray gene expression profiling was performed. R studio analysis tool was used to detect differentially expressed genes (DEGs) with |logFC| ≥ 2 as the cut-off criterion. The differentially expressed genes (DEGs) in the Deg-AZM-treated and control groups were enriched through GO analysis by using the GSEA software.

2020-08-12 | GSE156032 | GEO

cDNA (Cepko BMAP) experiments for cross-platform study

Project description:Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than “in-house” arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms. Keywords: cross platform microarrays

2006-06-01 | GSE4832 | GEO

Affymetrix experiments for cross-platform study including site 2 data

2006-06-01 | GSE4830 | GEO

ABI experiments for cross-platform study

2006-06-01 | GSE4829 | GEO

Cross-platform study

Project description:Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and in house platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms. This SuperSeries is composed of the SubSeries listed below.

2006-06-01 | GSE4854 | GEO

Mergen experiments for cross-platform study including site 2 data

2006-06-01 | GSE4837 | GEO