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Using high-density exon arrays to profile gene expression in closely related species (Exon 1.0 ST)

ABSTRACT: Global comparisons of gene expression profiles between species provide significant insight into gene regulation, evolutionary processes, and disease mechanisms. In this work, we describe a flexible and intuitive approach for global expression profiling of closely related species, using high-density exon arrays designed for a single reference genome. The high-density probe coverage of exon arrays allows us to select the identical set of perfect-match probes for measuring expression levels of orthologous genes. This eliminates a serious confounding factor in probe affinity effects of species-specific microarray probes, and enables direct comparisons of estimated expression indexes across species. Keywords: analysis of gene expression in tissues

ORGANISM(S): Homo sapiens Pan troglodytes

PROVIDER: GSE15626 | GEO | 2009/05/05

SECONDARY ACCESSION(S): PRJNA122935

REPOSITORIES: GEO

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Using high-density exon arrays to profile gene expression in closely related species (Exon 1.0 ST)

Project description:Global comparisons of gene expression profiles between species provide significant insight into gene regulation, evolutionary processes, and disease mechanisms. In this work, we describe a flexible and intuitive approach for global expression profiling of closely related species, using high-density exon arrays designed for a single reference genome. The high-density probe coverage of exon arrays allows us to select the identical set of perfect-match probes for measuring expression levels of orthologous genes. This eliminates a serious confounding factor in probe affinity effects of species-specific microarray probes, and enables direct comparisons of estimated expression indexes across species. Keywords: analysis of gene expression in tissues We conducted Human Exon 1.0 array profiling of RNAs from three chimpanzee cerebellums and three chimpanzee livers

2009-05-04 | E-GEOD-15626 | biostudies-arrayexpress

Using high-density exon arrays to profile gene expression in closely related species (HJAY)

2009-05-05 | GSE15665 | GEO

Using high-density exon arrays to profile gene expression in closely related species (HJAY)

Project description:Global comparisons of gene expression profiles between species provide significant insight into gene regulation, evolutionary processes, and disease mechanisms. In this work, we describe a flexible and intuitive approach for global expression profiling of closely related species, using high-density exon arrays designed for a single reference genome. The high-density probe coverage of exon arrays allows us to select the identical set of perfect-match probes for measuring expression levels of orthologous genes. This eliminates a serious confounding factor in probe affinity effects of species-specific microarray probes, and enables direct comparisons of estimated expression indexes across species. Keywords: analysis of gene expression in tissues We conducted Affymetrix Human Exon Junction array (HJAY array) profiling of RNAs from human, chimpanzee and rhesus macaque cerebellums, with three replicates per species.

2010-05-19 | E-GEOD-15665 | biostudies-arrayexpress

Exon-level summary data from Affymetrix Human Exon 1.0 ST array

Project description:The Affymetrix Human Exon 1.0 ST array was used to measure differential splicing patterns in archived RNA isolated from 26 of 80 children (11 Rejectors and 15 Non-Rejectors). The exon-level probe summaries reported in this series were computed using the Affymetrix Power Tools (APT) software and 'rma-sketch' normalization method. Keywords: Affymetrix 1.0 ST exon array; exon-level analysis

2008-09-15 | GSE11360 | GEO

Using high-density exon arrays to profile gene expression in closely related species

Project description:This SuperSeries is composed of the following subset Series: GSE15626: Using high-density exon arrays to profile gene expression in closely related species (Exon 1.0 ST) GSE15665: Using high-density exon arrays to profile gene expression in closely related species (HJAY) Refer to individual Series

2009-05-04 | E-GEOD-15666 | biostudies-arrayexpress

Gene-level summary data from Affymetrix Human Exon 1.0 ST array

Project description:The Affymetrix Human Exon 1.0 ST array was used to measure differential splicing patterns in archived RNA isolated from 26 of 80 children (11 Rejectors and 15 Non-Rejectors). The gene-level probe summaries reported in this series were computed using the Affymetrix Power Tools (APT) software and 'rma-sketch' normalization method. Keywords: Affymetrix 1.0 ST exon array; gene-level analysis

2008-09-15 | GSE11359 | GEO

Affymetrix Research Exon Array Tissue Panel Data

Project description:Manuscript Title: Discovery of tissue-specific exons using comprehensive human exon microarrays We have designed a high-density oligonucleotide microarray with probesets for more than one million annotated and predicted exons in the human genome. Using these arrays and a simple algorithm that normalizes exon signal to signal from the gene as a whole, we have identified tissue-specific exons from a panel of 16 different normal adult tissues. Pair-wise comparisons between the tissues suggest that 75% of detected genes are differentially alternatively spliced. We also demonstrate how an inclusive exon microarray can be used to discover novel alternative splicing events. As examples, 15 new tissue-specific exons from 9 genes were validated by RT-PCR and sequencing. Keywords: exon analysis

2007-01-01 | GSE5791 | GEO

Evaluation of the Affymetrix Brassica Exon 1.0 ST array

Project description:The aim of the experiment was to evaluate the performance of the Affymetrix Brassica Exon 1.0 ST array. Root and leaf samples from Brassica rapa line R-O-18 were compared. The same RNA samples were hybridised to the Agilent Brassica array, to compare the performance of the two arrays.

2010-09-10 | GSE23141 | GEO

Using high-density exon arrays to profile gene expression in closely related species

Project description:Using high-density exon arrays to profile gene expression in closely related species

| PRJNA115613 | ENA

Affymetrix Human Exon 1.0 ST array analysis of lymphoblastoid cell lines

Project description:This experiment accompanies the main analysis using a custom MHC array to define the first high-resolution, strand-specific transcriptional map of the MHC, defining differences in gene expression for three common haplotypes associated with autoimmune disease. Unstimulated samples for each haplotype were hybridised to Affymetrix Human Exon 1.0 ST arrays as well the custom MHC array. Exon array data were used to assess the concordance of signal obtained from the two platforms and to investigate the extent of alternative splicing in the MHC, and how it compares to the rest of the genome.

2011-05-23 | GSE22454 | GEO

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