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Sample GSM1683171 Query DataSets for GSM1683171
Status Public on Feb 01, 2016
Title LM16_rep2
Sample type RNA
 
Source name melanoma cell line derived from nodal metastasis
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
Treatment protocol The PLX4032-resistant cell line variant LM16-R was generated by repeated exposures to PLX4032 (3 µM) until the onset of resistance.
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.
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.
Label Cy3
Label protocol Total RNA from each sample was labeled according to the manufacturers recommendations.
 
Hybridization protocol Standard Agilent hybridization protocol
Scan protocol Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).
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.
 
Submission date May 13, 2015
Last update date Feb 01, 2016
Contact name Matteo Dugo
E-mail(s) [email protected]
Organization name IRCCS Ospedale San Raffaele
Department Department of Medical Oncology
Street address via Olgettina 60
City Milan
ZIP/Postal code 20132
Country Italy
 
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

Data table header descriptions
ID_REF
VALUE log2 quantile-normalized data

Data table
ID_REF VALUE
Blank 7.425478188
dmr_285 11.4950735
dmr_3 13.83421604
dmr_308 9.327263748
dmr_316 9.334211307
dmr_31a 10.67787608
dmr_6 13.29429378
hsa-let-7a-5p 11.56366098
hsa-let-7a-3p 9.336881654
hsa-let-7b-5p 10.29682776
hsa-let-7b-3p 9.359710614
hsa-let-7c 9.802146085
hsa-let-7c*_v16.0 9.264721398
hsa-let-7d-5p 9.773788979
hsa-let-7d-3p 9.286328419
hsa-let-7e-5p 9.913440657
hsa-let-7e-3p 9.272426255
hsa-let-7f-5p 10.93386333
hsa-let-7f-1-3p 9.386099292
hsa-let-7f-2-3p 9.31462713

Total number of rows: 1541

Table truncated, full table size 39 Kbytes.




Supplementary file Size Download File type/resource
GSM1683171_US11103886_253575810081_S01_miRNA_107_Sep09_1_2.txt.gz 3.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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