GEO DataSets

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL570 GPL11154

18 Samples

Download data: CEL, TXT

(Submitter supplied) 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:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

9 Samples

Download data: CEL

(Submitter supplied) RNA-Seq has been increasingly used for the quantification and characterization of transcriptomes. The ongoing development of the technology promises the more accurate measurement of gene expression. However, its benefits over widely accepted microarray technologies have not been adequately assessed, especially in toxicogenomics studies. The goal of this study is to enhance the scientific community's understanding of the advantages and challenges of RNA-Seq in the quantification of gene expression by comparing analysis results from RNA-Seq and microarray data on a toxicogenomics study. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10287

8 Samples

Download data: TXT

(Submitter supplied) C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6885 GPL1261

44 Samples

Download data: CEL, TXT

(Submitter supplied) Microarrays have been widely used for the analysis of gene expression and several commercial platforms are available. The combined use of multiple platforms can overcome the inherent biases of each approach, and may represent an alternative that is complementary to RT-PCR for identification of the more robust changes in gene expression profiles. In this paper, we combined statistical and functional analysis for the cross platform validation of two oligonucleotide-based technologies, Affymetrix (AFFX) and Applied Biosystems (ABI), and for the identification of differentially expressed genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL1426

12 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6097 GPL570

20 Samples

Download data: CEL, TXT

(Submitter supplied) The present study was conducted to compare the ability of Affymetrix and Illumina microarray technologies to characterize the differential gene expression profiles of human monocytes and monocyte-derived-macrophages. Keywords: Type Cross-platform comparison Summary

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3554

Platform:

GPL570

10 Samples

Download data: CEL

(Submitter supplied) In this study we analyzed the gene expression profiles of human monocytes and monocyte-dervied-macrophages. Keywords: Gene expression profiling

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3553

Platform:

GPL1946

96 Samples

Download data: GPR

(Submitter supplied) The present study was conducted to compare the ability of Affymetrix and Illumina microarray technologies to characterize the differential gene expression profiles of human monocytes and monocyte-derived-macrophages. Keywords: Cross-platform comparison

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3555

Platform:

GPL6097

10 Samples

Download data: TXT

Comparison of monocytes and macrophages. Samples obtained from patients with acute coronary syndrome. Results compared to the performance of Affymetrix arrays (GDS3554). The result from two-color arrays (GDS3553) was used as a reference for the Illumina and Affymetrix arrays.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 cell type, 5 individual sets

Platform:

GPL6097

Series:

GSE10213

10 Samples

Download data: TXT

Comparison of monocytes and macrophages. Samples obtained from patients with acute coronary syndrome. Results compared to the performance of Illumina arrays (GDS3555). The result from two-color arrays (GDS3553) was used as a reference for the Illumina and Affymetrix arrays.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 cell type, 5 individual sets

Platform:

GPL570

Series:

GSE11430

10 Samples

Download data: CEL

Comparison of monocytes and macrophages. Samples obtained from 86 patients with acute coronary syndrome. Results used as a reference to compare the performance of Affymetrix (GDS3554) and Illumina (GDS3555) arrays.

Organism:

Homo sapiens

Type:

Expression profiling by array, log ratio, 2 cell type, 48 individual, 2 protocol sets

Platform:

GPL1946

Series:

GSE10220

96 Samples

Download data: GPR

(Submitter supplied) Male Sprague Dawley rats were treated orally for 5 days with reference hepatotoxicants, each at a single dose level, alpha-naphthylisothiocyanate 100mg/kg (vehicle 5ml/kg corn oil); carbon tetrachloride 1582mg/kg (vehicle 5ml/kg corn oil); methylenedianiline 100mg/kg (vehicle 35% ethanol); acetaminophen 1000mg/kg (vehicle 2ml/kg corn oil); diclofenac 10mg/kg (vehicle 10ml/kg water)

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20084

26 Samples

Download data: TXT

(Submitter supplied) Male Sprague Dawley rats were treated orally for 5 days with reference hepatotoxicants, each at a single dose level alpha-naphthylisothiocyanate 100mg/kg (vehicle 5ml/kg corn oil); carbon tetrachloride 1582mg/kg (vehicle 5ml/kg corn oil); methylenedianiline 100mg/kg (vehicle 35% ethanol); acetaminophen 1000mg/kg (vehicle 2ml/kg corn oil); diclofenac 10mg/kg (vehicle 10ml/kg water)

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

26 Samples

Download data: CEL

(Submitter supplied) High throughput sequencing is a powerful tool to investigate complex cellular phenotypes in functional genomics studies. Sequencing of transcriptional molecules, RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared to traditional expression analysis based on microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in analysis of RNA-seq data and to cross-compare the results with those obtained through a microarray platform. more...

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae CEN.PK113-7D; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

6 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

5 related Platforms

90 Samples

Download data: GPR, TXT

(Submitter supplied) Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

18 Samples

Download data: TXT

(Submitter supplied) Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL8179

18 Samples

Download data: TXT

(Submitter supplied) Microarray technology applied to miRNA profiling is a promising tool in many research fields. At present, only few studies have addressed intra- and inter-platform reproducibility by using tissues/cell-lines of different origin to maximize differences in miRNA content. Although the approach might provide an useful system to address technical issues since, for sure, a huge modulation can be evaluated, it does not reflect the common experimental practice in laboratory. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14767

18 Samples

Download data: TXT