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| 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
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| 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
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| 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.
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| Contributor(s) |
Acevedo LG, Bieda MC, Green R, Farnham PJ |
| Citation(s) |
18413731 |
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| Submission date |
Mar 14, 2008 |
| Last update date |
Feb 15, 2013 |
| Contact name |
Mark Bieda |
| E-mail(s) |
markb7002000@yahoo.com
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| Organization name |
University of Calgary
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| Department |
Biochemistry and Molecular Biology
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| Lab |
Bieda
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| Street address |
3330 Hospital Dr NW
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| City |
Calgary |
| State/province |
AB |
| ZIP/Postal code |
T2N4N1 |
| Country |
Canada |
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| Platforms (4)
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| GPL3930 |
Nimblegen human 5K promoter array 2 |
| GPL4704 |
Nimblegen Human 5K promoter array 1 |
| GPL6102 |
Illumina human-6 v2.0 expression beadchip |
| GPL6255 |
Illumina humanRef-8 v2.0 expression beadchip |
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| Samples (45)
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| GSM272101 |
Array 88345 Promoter 1/Patient2/POLII ab |
| GSM272102 |
Array 87597 Promoter 2/Patient2/POLII ab |
| GSM272103 |
Promoter 1/Patient2/POLII Tumor liver |
| GSM272104 |
Promoter 2/Patient2/POLII Tumor liver |
| GSM272838 |
Normal Liver, Patient 2, me3K27 Promoter 1 Array, array 88819 |
| GSM272855 |
Normal Liver, Patient 2, me3K27 Promoter 2 Array, array 81470 |
| GSM272856 |
Tumor Liver, Patient 2, me3K27 Promoter 2 Array, array 87651 |
| GSM272857 |
Tumor Liver, Patient 2, me3K27 Promoter 1 Array, array 88452 |
| GSM273022 |
Normal Liver, Patient 4, POLII 1 Array, array 1859302 |
| GSM273025 |
Normal Liver, Patient 4, POLII 2 Array, array 1859702 |
| GSM273026 |
Normal Liver, Patient 4, H3me3K9 1 Array, array 1860902 |
| GSM273027 |
Normal Liver, Patient 4, H3me3K9 2 Array, array 1861102 |
| GSM276183 |
Tumor Liver, Patient 2, 3meK9 1 Array, array 1528802 |
| GSM276184 |
Normal Liver, Patient 1, 3meK9 2 Array, array 1557302 |
| GSM276185 |
Normal Liver, Patient 4, H3me3K27 1 Array, array 1860402 |
| GSM276186 |
Normal Liver, Patient 1, H3me3K27 2 Array, array 85219 |
| GSM276187 |
Normal Liver, Patient 1, POLII 1 Array, array 87639 |
| GSM276188 |
Tumor Liver, Patient 1, H3me3K27 1 Array, array 88833 |
| GSM276189 |
Normal Liver, Patient 1, H3me3K27 2 Array, array 95587 |
| GSM276190 |
Normal Liver, Patient 2, 3meK9 1 Array, array 1528902 |
| GSM276191 |
Normal Liver, Patient 2, 3meK9 2 Array, array 1558102 |
| GSM276192 |
Normal Liver, Patient 4, H3me3K27 2 Array, array 1860702 |
| GSM276193 |
Tumor Liver, Patient 1, H3me3K27 1 Array, array 85222 |
| GSM276194 |
Tumor Liver, Patient 1, POLII 2 Array, array 87658 |
| GSM276195 |
Normal Liver, Patient 1, POLII 1 Array, array 89040 |
| GSM276196 |
Tumor Liver, Patient 1, H3me3K27 2 Array, array 96083 |
| GSM276197 |
Tumor Liver, Patient 1, 3meK9 1 Array, array 1531402 |
| GSM276198 |
Tumor Liver, Patient 2, 3meK9 2 Array, array 1558302 |
| GSM276199 |
Tumor Liver, Patient 1, H3me3K27 2 Array, array 81475 |
| GSM276200 |
Tumor Liver, Patient 1, POLII 1 Array, array 85230 |
| GSM276201 |
Tumor Liver, Patient 1, POLII 1 Array, array 88346 |
| GSM276202 |
Tumor Liver, Patient 1, POLII 2 Array, array 89050 |
| GSM276203 |
Normal Liver, Patient 1, 3meK9 1 Array, array 1531602 |
| GSM276204 |
Tumor Liver, Patient 1, 3meK9 2 Array, array 1558902 |
| GSM276205 |
Normal Liver, Patient 1, H3me3K27 1 Array, array 81601 |
| GSM276206 |
Normal Liver, Patient 1, POLII 2 Array, array 85233 |
| GSM276207 |
Normal Liver, Patient 1, H3me3K27 1 Array, array 88349 |
| GSM276208 |
Normal Liver, Patient 1, POLII 2 Array, array 95568 |
| GSM278088 |
array #1740115250_E, Normal Liver RNA Patient 1 |
| GSM290549 |
array #1740115250_A, Purified Normal Hepatocytes, patient 5 |
| GSM290550 |
array #1740115250_F, Tumor Liver RNA Patient 1 |
| GSM290551 |
array #1740115250_G, Normal Liver RNA patient 3 |
| GSM290552 |
array #1740115250_H, Tumor Liver RNA patient 3 |
| GSM296418 |
Normal Liver RNA (not cancer-related), Patient 4 |
| GSM296419 |
Normal Liver RNA (not cancer-related), Patient 4_replicate |
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| Relations |
| BioProject |
PRJNA107327 |
| 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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