GEO DataSets

(Submitter supplied) The recent development within high-throughput technologies for expression profiling has allowed for parallel analysis of transcriptomes and proteomes in biological systems such as comparative analysis of transcript and protein levels of tissue regulated genes. Until now, such studies of have only included microarray or short length sequence tags for transcript profiling. Furthermore, most comparisons of transcript and protein levels have been based on absolute expression values from within the same tissue and not relative expression values based on tissue ratios. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL6173

18 Samples

Download data: GPR

(Submitter supplied) A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here, different Treatments/Conditions based on different Arabidopsis tissues were used for three different platforms include MPSS, Affymetrix and Agilent. Keywords: MPSS, Affymetrix, Agilent

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL888 GPL5800 GPL198

44 Samples

Download data: CEL, TIFF, TXT

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

Organism:

Danio rerio

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL15180

7 Samples

Download data: TSV, TXT

(Submitter supplied) We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes for untreated fish. The transcriptomes were also compared for fish injected in the yolk with Mycobacterium marinum

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

3 Samples

Download data: TSV

(Submitter supplied) We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL15180

4 Samples

Download data: TXT

(Submitter supplied) SAGE analysis of fully grown ovarian follicles has been carried out to supply a resource for identification of important molecules involved in vertebrate oogenesis and in early stages of embryonic development. Keywords: SAGE

Organism:

Danio rerio

Type:

Expression profiling by SAGE

Platform:

GPL3209

1 Sample

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(Submitter supplied) High-throughput systems for gene expression profiling have been developed and matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised regarding data comparability and agreement across technologies. Within an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel Signature Sequencing). more...

Organism:

Mus musculus

Type:

Expression profiling by array

7 related Platforms

45 Samples

Download data: CEL, TIFF, TXT

(Submitter supplied) Sunflower is an important source of vegetable oil worlwide. A differential organ-specific sunflower ESTs was previously generated by a subtractive hybridization method, including a considerable number of abiotic stress associated sequences. The objective of this work is to analyze the sunflower gene expression of previously identified candidate genes under a comprehensive microarray analysis of the leaf transcriptoma under cold and salinity stresses, considering the impacts of these abiotic stresses on sunflower yield in many productive areas. more...

Organism:

Helianthus annuus

Type:

Expression profiling by array

Platform:

GPL4366

18 Samples

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(Submitter supplied) Parkinson disease (PD) is a neurodegenerative disease characterized by the accumulation of alpha-synuclein (SNCA) and other proteins in aggregates termed “Lewy Bodies” within neurons. PD has both genetic and environmental risk factors, and while processes leading to aberrant protein aggregation are unknown, past work points to abnormal levels of SNCA and other proteins. Although several genome-wide studies have been performed for PD, these have focused on DNA sequence variants by genome-wide association studies (GWAS) and on RNA levels (microarray transcriptomics), while genome-wide proteomics analysis has been lacking. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

73 Samples

Download data: RDATA, TXT

(Submitter supplied) Background: Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems. Results: Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity from the same experimental vineyard and ˚Brix-to-titratable acidity ratio. more...

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL17894

50 Samples

Download data: PAIR, 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) Microarrays revolutionized biological research by enabling gene expression comparisons on a transcriptome-wide scale. Microarrays, however, do not estimate absolute expression level accurately. At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed by microarray design, its potential to estimate absolute transcript levels is unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

7 Samples

Download data: CEL

(Submitter supplied) Comparative gene expression profiling of a) above-ground tissues of three fruiting species (P. cheesemanii, ch, P. exile, ex, P. novae-zelandiae, nz), b) above-ground tissues of two rosette stage species (P. fastigiatum, fa, P. enysii, en) and c) roots of all five species using heterologous A. thaliana microarrays

Organism:

Arabidopsis thaliana; Pachycladon cheesemanii; Pachycladon fastigiatum; Pachycladon exile; Pachycladon novaezelandiae; Pachycladon enysii

Type:

Expression profiling by array

Platform:

GPL9670

36 Samples

Download data: GPR

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL13534 GPL6244

180 Samples

Download data: CEL

(Submitter supplied) This study identified DNA methylation patterns that were associated with tumor subtypes, disease outcome, and distinct metabolome and gene expression patterns.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

72 Samples

Download data: TXT

(Submitter supplied) This study identified DNA methylation patterns that were associated with tumor subtypes, disease outcome, and distinct metabolome and gene expression patterns.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

108 Samples

Download data: CEL

(Submitter supplied) Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is complicated by the need to minimize artifacts associated with highly abundant globin RNA transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL201

24 Samples

Download data: CEL, CHP

(Submitter supplied) BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether RNA-Seq could be used to identify IPF expression profiles from archived Formalin-Fixed Paraffin-Embedded (FFPE) lung fibrotic tissue. RESULTS: We isolated total RNA from 7 IPF and 5 control FFPE lung tissues (median archived time 6 years) and performed 50 bp paired-end sequencing on Illumina 2000 HiSeq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

11 Samples

Download data: TXT

(Submitter supplied) Background: Previous studies comparing quantitative proteomics and microarray data have generally found poor correspondence between the two. We hypothesised that this might in part be because the different assays were targeting different parts of the expressed genome and might therefore be subjected to confounding effects from processes such as alternative splicing. Results: Using a genome database as a platform for integration, we combined quantitative protein mass spectrometry with Affymetrix Exon array data at the level of individual exons. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

6 Samples

Download data: CEL

(Submitter supplied) Jatropha curcas, a tropical shrub, is an attractive biofuel crop, which produces seeds with a high content of oil and protein. Most J. curcas accessions contain a range of toxins and anti-nutritional compounds, which are unfavorable for human consumption and animal feed. With the goal of better understanding the development of its seeds and to improve Jatropha`s agronomic performance, a two-step approach was performed: 1) generation of the entire transcriptome of six different developmental stages of J. more...

Organism:

Jatropha curcas

Type:

Expression profiling by array

Platform:

GPL24563

31 Samples

Download data: TXT