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Sample GSM3305847 Query DataSets for GSM3305847
Status Public on Jul 16, 2019
Title A375 Parental, biological rep1
Sample type RNA
 
Source name melanoma cell line derived from Lymph Node Metastasis
Organism Homo sapiens
Characteristics cell line: A375
sample type: BRAFV600E parental cells sensitive to BRAF inhibitors
phenotype: Parental cell line
Treatment protocol A375 and A375R cells were removed from culture, seeded into 10-cm dishes, and maintained in CM for 48 h. The cells were then detached with a solution of EDTA in PBS, washed in PBS and frozen in a RNA-later®/PBS solution.
Growth protocol A375 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 50 m/ml gentamicin (Complete Medium, CM). The A375R cell line was maintained in CM supplemented with 1.5 mM dabrafenib
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol reagent (Invitrogen) and mirVana miRNA isolation kit (Ambion) following the manufacturers protocol. RNA quantity and quality were determined using a Nanodrop-1000 spectrophotometer (Nanodrop Technology) and Agilent 2100 Bioanalyzer.
Label biotin
Label protocol 130-1000 ng of total of RNA was biotin labeled using the FlashTag™ HSR RNA labeling kit for Affymetrix GeneChip™ miRNA 3.1 Array Strip hybidization.
 
Hybridization protocol Following biotinylation, these fragments were hybridized for 20 hr at 45°C on Affymetrix miRNA 3.1 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for miRNA Array strips.
Scan protocol GeneChip were finally scanned using GeneAtlas Scanner.
Data processing Affymetrix Expression Console. Data were preprocessed following the RMA procedure using quantile normalization
 
Submission date Jul 25, 2018
Last update date Jul 16, 2019
Contact name Adriana Agnese Amaro
E-mail(s) adriana.amaro@hsanmartino.it
Phone +390105558312
Organization name IRCCS Ospedale Policlinico SAN MARTINO - IST - NATIONAL CANCER RESEARCH INSTITUTE
Department Molecular Pathology
Street address Largo Rosanna Benzi 10
City Genoa
ZIP/Postal code 16132
Country Italy
 
Platform ID GPL16384
Series (1)
GSE117666 miRNA expression profiling of the A375 melanoma cell line and its dabrafenib-resistant A375R sub-line.

Data table header descriptions
ID_REF
VALUE Quantification
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
14q0_st 0.680946 0.991735
14qI-1_st 1.38445 0.673264
14qI-1_x_st 0.918428 0.504782
14qI-2_st 1.35012 0.0907697
14qI-3_x_st 1.1771 0.234318
14qI-4_st 1.17066 0.849741
14qI-4_x_st 1.06535 0.939608
14qI-5_st 1.52265 0.567191
14qI-6_st 1.19452 0.216146
14qI-6_x_st 1.35006 0.291197
14qI-7_st 1.03836 0.941764
14qI-8_st 1.00316 0.927478
14qI-8_x_st 1.49916 0.299248
14qI-9_x_st 0.950006 0.832712
14qII-10_st 1.31051 0.256985
14qII-10_x_st 1.27452 0.140543
14qII-11_st 1.34523 0.807672
14qII-11_x_st 1.26993 0.953811
14qII-12_st 1.20732 0.736105
14qII-12_x_st 0.951641 0.868682

Total number of rows: 5683

Table truncated, full table size 197 Kbytes.




Supplementary file Size Download File type/resource
GSM3305847_TG33.ga.cel.gz 943.0 Kb (ftp)(http) CEL
GSM3305847_TG33.ga.datri.rma-dabg.chp.gz 71.8 Kb (ftp)(http) CHP
Processed data included within Sample table

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