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| Status |
Public on Nov 22, 2011 |
| Title |
Simultaneous analysis of tumor and stromal gene expression profiles from xenograft models |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Identifying the gene expression alterations that occur in both the tumor and stroma is essential to understanding tumor biology. We have developed a dual-species microarray analysis method that allows the dissection of both tumor and stromal gene expression profiles from xenograft models, based on limited interspecies cross-hybridization on Illumina gene expression beadchips. This methodology allows for simultaneous genome-wide analysis of gene expression profiles of both tumor cells and the associated stromal tissue.
Data is provided regarding the crosshybridization of mouse liver RNA on human microarray, and MDA-MB-231 breast cancer cell line RNA on mouse microarray. Data is also provided for comparisons of MDA-MB-231 gene expression in vitro vs. in vivo, and mouse liver gene expression in control mice vs. stroma from MDA-MB-231 xenograft liver metastasis in tumor bearing mice
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| Overall design |
A total of 18 samples were analyzed. Samples consist of 6 different types with each type in triplicate. Types are (1) MDA-MB-231 cell line grown in vitro and arrayed on mouse chips, (2) mouse liver from NOD/SCID mice arrayed on human chips, (3) MDA-MB-231 cell line grown in vitro arrayed on human chips, (4) MDA-MB-231 xenograft liver metastasis arrayed on human chips, (5) mouse liver from NOD/SCID mice arrayed on mouse chips, and (6) MDA-MB-231 xenograft liver metastasis arrayed on mouse chips. The overall design had three objectives: (1) to determine crosshybridizing probes based on sample types 1, 2, 3, and 5, (2) detect stromal and tumor expression using sample types 4 and 6, and (3) determine genes differentially expressed in tumor or metastasis compared to normal by comparing sample types 3 and 4 and comparing sample types 1 and 5.
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| Contributor(s) |
Clarke JL, Iorns E |
| Citation(s) |
21947683 |
| Submission date |
Jul 27, 2011 |
| Last update date |
Jan 16, 2019 |
| Contact name |
Jennifer Clarke |
| Organization name |
University of Miami
|
| Department |
Epidemiology and Public Health
|
| Lab |
Division of Biostatistics
|
| Street address |
1120 NW 14th Street
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
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| Platforms (2) |
| GPL6887 |
Illumina MouseWG-6 v2.0 expression beadchip |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA146167 |
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