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Series GSE10842 Query DataSets for GSE10842
Status Public on Jun 04, 2008
Title Tumor Liver vs Normal Liver: ChIP-chip and RNA expression
Organism Homo sapiens
Experiment type Expression profiling by genome tiling array
Summary There is widespread interest in efficient characterization of differences between tumor and normal samples. Here, we demonstrate an effective methodology for genome-scale characterization of tumors.

Using matched normal and tumor samples from liver cancer patients, as well as non-cancer-related normal liver tissue, we first determined changes in gene expression as monitored on RNA expression arrays. We identified several hundred mRNAs that were consistently changed in the tumor samples.

To characterize the mechanisms responsible for creation of the tumor-specific transcriptome, we performed ChIP-chip experiments to assay binding of RNA polymerase II, H3me3K27, and H3me3K9 in 25,000 promoter regions. These experiments identified changes in active and silenced regions of the genome in the tumor cells.

Finally, we used a “virtual comparative genomic hybridization” (vCGH) method to identify copy number alterations in the tumor samples.

Through comparison of RNA Polymerase II binding, chromatin structure, and copy number changes, we suggest that the major contributor to creation of the liver tumor transcriptome was changes in gene copy number.
Keywords: ChIP-chip, gene expression, CGH
Overall design Source material: Liver samples from human liver cancer patients, normal human liver samples, liver cell lines and normal human hepatocytes.
Experiments: ChIP-chip with abs against POLII, H3me3K27, and H3me3K9, and DNA methylation using NimbleGen 5 kb promoter arrays. RNA expression from the listed sources using Illumina Bead system.
Compare normal liver to tumor liver and normal cell lines to tumor cell lines.
Contributor(s) Acevedo LG, Bieda MC, Green R, Farnham PJ
Citation(s) 18413731
Submission date Mar 14, 2008
Last update date Feb 15, 2013
Contact name Mark Bieda
Organization name University of Calgary
Department Biochemistry and Molecular Biology
Lab Bieda
Street address 3330 Hospital Dr NW
City Calgary
State/province AB
ZIP/Postal code T2N4N1
Country Canada
Platforms (4)
GPL3930 Nimblegen human 5K promoter array 2
GPL4704 Nimblegen Human 5K promoter array 1
GPL6102 Illumina human-6 v2.0 expression beadchip
Samples (45)
GSM272101 Array 88345 Promoter 1/Patient2/POLII ab
GSM272102 Array 87597 Promoter 2/Patient2/POLII ab
GSM272103 Promoter 1/Patient2/POLII Tumor liver
BioProject PRJNA107327

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Supplementary file Size Download File type/resource
GSE10842_RAW.tar 1.0 Gb (http)(custom) TAR (of CSV, IDAT, LOCS, TIFF, TXT, XML)
Processed data included within Sample table
Processed data not applicable for this record

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