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Series GSE19830 Query DataSets for GSE19830
Status Public on Mar 08, 2010
Title Expression data from pure/mixed brain, liver and lung to test feasability and sensitivity of statistical deconvolution
Organism Rattus norvegicus
Experiment type Expression profiling by array
Summary Tissues are often made up of multiple cell-types. Blood, for example, contains many different cell-types, each with its own functional attributes and molecular signature. In humans, because of its accessibility and immune functionality, blood cells have been used as a source for RNA-based biomarkers for many diseases. Yet, the proportions of any given cell-type in the blood can vary markedly, even between normal individuals. This results in a significant loss of sensitivity in gene expression studies of blood cells and great difficulty in identifying the cellular source of any perturbations. Ideally, one would like to perform differential expression analysis between patient groups for each of the cell-types within a tissue but this is impractical and prohibitively expensive.
To test the relationship between measured gene expression in mixed samples and the expression of genes in the isolated pure subsets, we begin with a situation in which all factors are known. Tissue samples from the brain, liver and lung of a single rat were analyzed using expression arrays (Affymetrix) in triplicate. Homogenates of those three tissues were then mixed together at the cRNA level. We then measured the gene expression pattern of each mixed sample. Such mixtures mimic the common scenario in which biological samples in a dataset are heterogeneous and vary in the relative frequency of the component subsets from one another.
Overall design We mixed rat brain, liver and lung biospecimens derived from one animal at the cRNA homogenate level in different proportions. 3 technical replicates each. Snap frozen rat liver and brain was kept frozen while cutting it into pieces. cDNA synthesis and labeling was done with a starting amount of 1 μg, using the Affymetrix Eukaryotic One-Cycle Target Hybridization. Washing, Staining and scanning protocol for Eukaryotic Cartridge Arrays with User-Prepared Buffers and Sloutions according to the technical manuals (Affymetrix GeneChip Expression, Analysis for Cartridge Arrays using the GCAS version 1.4, Affymetrix GeneChip Expression Analysis (P/N 701021,Rev. 5) , Affymetrix GeneChip Expression Wash, Stain and Scan (P/N 702731, Rev. 3) , following the manufacturer/s instructions. Data was RMA normalized.
Contributor(s) Shen-Orr SS, Staedtler F, Hartmann N, Letzkus M, Oakeley E
Citation(s) 20208531
Submission date Jan 11, 2010
Last update date Jul 31, 2017
Contact name Shai Shen-Orr
Organization name Stanford University
Street address 251 Campus Dr. Rm.X-251
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL1355 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array
Samples (42)
GSM495209 NUID-0000-0094-1609
GSM495210 NUID-0000-0094-1620
GSM495211 NUID-0000-0094-1631
BioProject PRJNA122165

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19830_RAW.tar 92.5 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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