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

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

PROVIDER: PRJNA115613 | ENA |

REPOSITORIES: ENA

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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

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

2009-05-05 | GSE15626 | GEO

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 (Exon 1.0 ST)

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

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

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

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

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

| PRJNA122927 | ENA

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2009-05-05 | GSE15666 | GEO

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

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 identical sets of perfect-match probes to measure 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. Using a newly designed Affymetrix exon array, with eight probes per exon for approximately 315,000 exons in the human genome, we conducted expression profiling in corresponding tissues from humans, chimpanzees and rhesus macaques. Quantitative real-time PCR analysis of differentially expressed candidate genes is highly concordant with microarray data, yielding a validation rate of 21/22 for human versus chimpanzee differences, and 11/11 for human versus rhesus differences. This method has the potential to greatly facilitate biomedical and evolutionary studies of gene expression in nonhuman primates and can be easily extended to expression array design and comparative analysis of other animals and plants.

| S-EPMC2709591 | biostudies-literature

High-density spatial transcriptomics arrays for in situ tissue profiling

Project description:High-density spatial transcriptomics arrays for in situ tissue profiling

| PRJNA540976 | ENA

A Systematic Comparison and Evaluation of High Density Exon Arrays and RNA-seq technology in Unraveling the Peripheral Blood Transcriptome of Sickle Cell Disease.

Project description:Sickle cell transcriptome was analyzed using whole blood clinical specimens on the Affymetrix Human Exon 1.0 ST arrays and Illumina’s deep sequencing technologies. Data analysis indicated a strong concordance (R=0.64) between exon array and RNA-seq in both gene level and exon level expression of transcripts. The magnitude of fold changes in the expression levels for the differentially expressed genes (p<0.05) was found to be higher in RNA-seq than microarrays. However, the arrays outperformed the sequencing technology in the detection of low abundant transcripts. In addition to examining the expression level changes of transcripts, RNA-seq technology was able to identify sequence variation in the expressed transcripts. We also demonstrate herein the ability of RNA-seq technology to discover novel expression outside of the annotated genes.

2012-07-06 | GSE31757 | GEO

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