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Status |
Public on Feb 01, 2016 |
Title |
LM16_rep2 |
Sample type |
RNA |
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Source name |
melanoma cell line derived from nodal metastasis
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Organism |
Homo sapiens |
Characteristics |
plx4032 sensitivity: Sensitive cell type: parental melanoma cell line derived from nodal metastasis and sensitive to PLX4032. Its genetic characterization has been reported in Vergani et al., Neoplasia 2011; 13(12):1132-42
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Treatment protocol |
The PLX4032-resistant cell line variant LM16-R was generated by repeated exposures to PLX4032 (3 µM) until the onset of resistance.
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Growth protocol |
The parental melanoma cell line LM16 and the resistant variant LM16-R were cultured in RPMI medium supplemented with 10% FCS, HEPES buffer, glutamine and antibiotics. Cells were grown for 72 hours before recovery for RNA extraction.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up with Ambion miRVANA kit according to the protocol provided by the manufacturer.
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Label |
Cy3
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Label protocol |
Total RNA from each sample was labeled according to the manufacturers recommendations.
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Hybridization protocol |
Standard Agilent hybridization protocol
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Scan protocol |
Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).
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Description |
parental melanoma cell line derived from nodal metastasis and sensitive to PLX4032. Its genetic characterization has been reported in Vergani et al., Neoplasia 2011; 13(12):1132-42
|
Data processing |
Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the AgiMicroRna package. microRNA-level processed signals were obtained using the RMA algorithm with quantile normalization.
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Submission date |
May 13, 2015 |
Last update date |
Feb 01, 2016 |
Contact name |
Matteo Dugo |
E-mail(s) |
[email protected]
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Organization name |
IRCCS Ospedale San Raffaele
|
Department |
Department of Medical Oncology
|
Street address |
via Olgettina 60
|
City |
Milan |
ZIP/Postal code |
20132 |
Country |
Italy |
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Platform ID |
GPL20194 |
Series (2) |
GSE68839 |
Gene and microRNA expression profiling of a melanoma cell line resistant to BRAF inhibitor PLX4032 compared to the parental sensitive counterpart (miRNA) |
GSE68841 |
Gene and microRNA expression profiling of a melanoma cell line resistant to BRAF inhibitor PLX4032 compared to the parental sensitive counterpart |
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