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| Status |
Public on Dec 14, 2012 |
| Title |
Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays [RNA-Seq] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In order to study molecular changes in the stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. This is particularly relevant to mouse tumor xenograft models where tumor, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor (human) and stromal (mouse) expression from mixed tumor-stromal samples in terms of the genes and pathways that are involved in cross-alignment (RNA-Seq) and cross-hybridization (microarrays).
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| Overall design |
Human samples consisted of total RNA obtained from MDA-MB-231 human breast carcinoma cell line and isolated from three independent cultures of sub-confluent MDA-MB-231 cell lines in exponential phase of growth. Mouse samples were obtained from NOD scid gamma mice, and normal lung tissue was harvested from three independent age-matched mice.
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| Contributor(s) |
Valdes C, Clarke J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Sep 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Camilo Valdes |
| Organization name |
University of Miami
|
| Department |
Center for Computational Science
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| Lab |
Bioinformatics and Computational Biology
|
| Street address |
Locator C-213. 1120 NW 14 Street
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| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
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| Platforms (3) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL16061 |
Illumina Genome Analyzer IIx (Homo sapiens; Mus musculus) |
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| Samples (19)
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| This SubSeries is part of SuperSeries: |
| GSE40892 |
Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays |
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| Relations |
| BioProject |
PRJNA175327 |
| SRA |
SRP015764 |
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