AffymetrixHuman Gene 2.0 ST Array
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ABSTRACT:
PROVIDER: PRJNA478427 | ENA |
REPOSITORIES: ENA
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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
2008-02-01 | GSE9819 | GEO
Project description:GeneChip® Mouse Gene 2.0 ST Array for C57BL/6 mouse skin dermal primary lymphatic endothelial cells (Ms LEC) and mouse lymphatic endothelial cell line SVEC4-10 GeneChip® Human Gene 2.0 ST Array for human primary lymphatic endothelial cells (Hu LEC) Total RNA from lymphatic cell line SVEC4-10 were used for GeneChip® Mouse Gene 2.0 ST Array.
2016-07-20 | GSE84551 | GEO
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
Project description:Exon Level Expression Profiling:HTA 2.0 array
| PRJNA814287 | ENA
Project description:Gene expression in glioblastoma cells from patients before treatment. The cells were inhibited or not for FGFR1. Glioblastoma are known to be aggressive and therapy-resistant tumors, due to the presence of glioblastoma stem cells (GSC) inside this heterogeneous tumor. We investigate here the involvement of FGFR1 in glioblastoma stem-like cells (GSLC) radioresistance mechanisms. We first demonstrated that the survival after irradiation was significantly diminished in FGFR1-silenced (FGFR1-) GSLC compared to control GSLC. The transcriptome analysis of GSLCs FGFR1(-) showed that FOX family members are differentially regulated by FGFR1 inhibition, particularly with an upregulation of FOXN3 and a downregulation of FOXM1. GSLC survival after irradiation was significantly increased after FOXN3 silencing and decreased after FOXM1 inhibition, showing opposite effects of FGFR1/FOX family members on cell response to ionizing radiation. Silencing FGFR1 or FOXM1 downregulated genes involved in mesenchymal transition such as GLI2, TWIST1, and ZEB1 in GSC. It also dramatically reduced GSLC migration, strongly suggesting that FGFR1/FOXM1 pathway which regulates GSLC radioresistance. Databases analysis confirmed that the combined expression of FGFR1/FOXM1/MELK/GLI2/ZEB1/TWIST1 is significantly associated with patients overall survival after chemo-radiotherapy treatment. All these results, associated with our previous conduced ones with differentiated cells, clearly established that FGFR1-FOXM1 dependent GSC radioresistance pathway is a central actor of GBM treatment resistance and a key target to inhibit in the aim to increase the sensitivity of GBM to the radiotherapy.
2018-06-29 | GSE116414 | GEO
Project description:The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized. The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array. The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized. The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array. Keywords: cross hybridization
2008-06-15 | GSE9531 | GEO
Project description:Gene expression profiles of adrenocortical carcinomas were analyzed using Affymetrix Human Gene 2.0 ST Array to identify homogeneous molecular subgroups
2014-04-29 | GSE49278 | GEO
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
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
Project description:We hybridized yeast RNA to the mouse 430 2.0 array to estimate the background binding for each probe.
2011-01-01 | GSE22975 | GEO