Drug Matrix Data - Affymetrix Arrays
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PROVIDER: PRJNA248180 | ENA |
REPOSITORIES: ENA
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Project description:Drug Matrix Data - Affymetrix Arrays
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Project description:Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays
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Project description:Cell and protein arrays have demonstrated remarkable utility in the high-throughput evaluation of biological responses; however, they lack the complexity of native tissue and organs and cannot replicate the environment of mature normal or diseased tissues. Here, we describe the development of tissue and organ extracellular matrix (ECM) arrays for screening biological outputs and systems analysis. Tissues and organs were chemically and mechanically processed and then formulated as particles without any enzymatic breakdown. The tissue ECM particles were spotted as two-dimensional tissue ECM arrays or incorporated with cells to generate three-dimensional cell-ECM microtissue arrays, and these methods were compatible with tissues prepared with varied processing techniques. The physical and biochemical properties, including the proteomic composition, of the tissue ECM arrays were characterized and compared with native tissues. The 2D arrays were validated through quantitative analysis of tissue-specific biological outputs of cell matrix production, cell adhesion and proliferation, and cell shape following culture with stem cells, cancer cells, and macrophages. Tissue-specific stem cell osteogenic differentiation on the arrays was comparable between 2D and 3D ECM environments, and revealed lung as an unexpected promoter of osteogenesis. Further gene ontology analysis of lung tissue ECM proteomics showed enrichment for families of proteins associated with skeletal development and osteogenesis. Stem cell biological outputs, along with cancer line adhesion and macrophage shape, were correlated with tissue proteomics, and network analysis identified several protein determinants of cell function. Our methodology enables broad screening of tissue and organ ECMs to connect tissue-specific composition with biological responses via systems analysis, providing a new resource for research and translation.
2015-09-28 | PXD002571 | Pride
Project description:The experiment was based on 3 arrays (3 Illumina HumanHap300 and 3 Affymetrix Genechip HindIII arrays) of each type being hybridized to a single pool which contained equal amounts of DNA from each of 384 individuals. The goal is to estimate a pooling allele frequency, the average frequency of allele 1, say, in the set of 384 individuals. After processing, the raw data are summarized to give pooling allele frequency estimates for each array. Abstract from paper comparing two arrays (one affy, one illumina) is as follows; Genome wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and contrasted Affymetrix Genechip HindIII and Illumina HumanHap300 arrays on the same DNA pools and show that the HumanHap300 arrays are substantially more efficient. In terms of effective sample size, HumanHap300 based pooling extracts >80% of the information available with individual genotyping (IG). In contrast, Genechip HindIII based pooling only extracts ~30% of the available information. With HumanHap300 arrays concordance with IG data is excellent. Guidance is given on best study design and it is shown that even after taking into account pooling error, one stage scans can be performed for >100 fold reduced cost compared with IG. With appropriately designed two stage studies, IG can provide confirmation of pooling results whilst still providing ~20 fold reduction in total cost compared with IG based alternatives. The large cost savings with Illumina HumanHap300 based pooling imply that future studies need only be limited by the availability of samples and not cost. Keywords: DNA pooling experiment
2007-11-06 | GSE9307 | GEO
Project description:Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array. Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array.
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