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| Status |
Public on Nov 03, 2016 |
| Title |
Identification of functional interactions through integration and systems analysis of matched gene and microRNA expression data across the Ludwig-Melbourne Melanoma (LM-MEL) Cell Line Panel |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
MicroRNAs contribute to metastatic progression in many cancers by modulation of phenotypic reprogramming processes such as epithelial-mesenchymal plasticity. However, it remains challenging to identify microRNA-mRNA interactions of functional significance at endogenous expression levels. The LM-MEL cell line panel comprises a large set of unique melanoma cell lines derived from largely metastatic melanoma tumours, as described in Behren et al, PCMR 2013 26(4):597-600 (PMID 23527996). For this study, 57 of the cell lines underwent matched gene expression (Illumina HT12v4 microarray) and small RNASeq (Illumina HiSeq) profiling in unperturbed conditions, generating a large dataset of matched gene and microRNA abundance data which was integrated with available phenotypic annotations covering several conditions of biological interest. We developed a novel systems analysis workflow to identify putative regulatory interactions suitable for subsequent validation.
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| |
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| Overall design |
Small RNA profiling of 57 cell lines of the LM-MEL panel using the Illumina HiSeq platform, with miRNA profiling performed subsequently using the miRanalyzer webserver interface (http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php)
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| |
|
| Contributor(s) |
Andrews M, Behren A |
| Citation(s) |
27852308 |
| |
| Submission date |
Nov 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Miles Andrews |
| E-mail(s) |
[email protected]
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Surgical Oncology
|
| Lab |
Wargo Lab
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (57)
|
|
| Relations |
| BioProject |
PRJNA352208 |
| SRA |
SRP092450 |
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