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

ABSTRACT: 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE11360 | GEO | 2008/09/15

SECONDARY ACCESSION(S): PRJNA109215

REPOSITORIES: GEO

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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

Evaluation of the Affymetrix Brassica Exon 1.0 ST array

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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.

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Affymetrix Human Exon 1.0 ST array assay of 15 human MLL-associated samples and 9 human normal bone marrow [HuEx-1_0-st]

Project description:To identify potential target genes of leukemia-related miRNAs such as miR-196b and miR-150 in human MLL-associated leukemia, we performed Affymetrix Human Exon 1.0 ST array assay of 15 human MLL-associated samples and 9 human normal bone marrow (including 3 each of CD34+, CD33+, and MNC) cell samples.

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Affymetrix Human Exon 1.0 ST array analysis of lymphoblastoid cell lines

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Exon-expression profiling of CD4+ T cells derived from HTLV-1-infected individuals with or without malignancy

Project description:T-cell clones were obtained by limiting dilution culture of PBMC of HTLV-1 carriers. Exon expression profiling was performed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions. Gene version of CEL files 01 to 12 are presented in GSE46518.

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Exon level expression data from the liver of adult control and Dhx32 homozygous mutant mice

Project description:We compared the whole mRNA transcript expression from control and homozygous mutant Dhx32 mice by Affymetrix Mouse Exon ST 1.0 Array ST to identify alternatively spliced mRNA transcripts We include exon level expression data from the liver of three control and three Dhx32 homozygous mutant mice

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Exon array data for patient-matched primary and metastatic colorectal samples

Project description:Samples were taken from surgically resected tumor specimens/metastases from patients with colorectal cancer. The expression profiles were determined using the Affymetrix GeneChip Human Exon 1.0 ST Array version 2.

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Comparisons of Affymetrix Whole-Transcript Human Gene 1.0 ST array with standard 3' expression arrays

Project description:The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3'™ based arrays: (1) it interrogates the entire mRNA transcript, and (2) it uses cDNA targets. To assess the impact of these differences on array performance, we performed series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both cRNA and cDNA targets were probed on the HG-U133 Plus 2.0 array. The results show that the overall reproducibility is best using the Gene 1.0 ST array. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. The Gene 1.0 ST is most concordant with the HG-U133 array hybridized with cDNA targets, thus showing the impact of the target type. Agreements are better between platforms with designs which choose probes from the 3' end of the gene. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array. Keywords: Cross-platform comparison

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2010-09-10 | E-GEOD-23141 | biostudies-arrayexpress

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