|
| Status |
Public on Apr 30, 2017 |
| Title |
GICAN |
| Sample type |
RNA |
| |
|
| Source name |
NB cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: neuroblastoma cell line GICAN
alk expression: ALK -
mycn status: single copy
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Neuroblastoma cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS),1% penicillin/streptomycin, 1% glutamine at 37°C, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA containing miRNA were extracted using miRNeasy kit (Qiagen), then quantification and quality control were performed on Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using Agilent RNA 6000 Nano Kit and Agilent Small RNA kit.
|
| Label |
Cy3
|
| Label protocol |
miRNA were labelled according Microarray System protocol v.2.4 (Agilent Technologies). Briefly Labeling Spike-In were added to 100 ng of total RNA, then dephosphorylated and labelled using miRNA Complete Labeling and Hyb Kit; after labeling samples were purified using Micro Bio-Spin 6 (Bio-Rad, Hercules, CA, USA).
|
| |
|
| Hybridization protocol |
After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on Human microRNA Microarray G4471A-029297 (Agilent Technologies) containing probes for 866 human microRNAs.
|
| Scan protocol |
After washing, slides were scanned by Agilent G2565CA scanner and images were processed by Feature Extraction software using Agilent HD_miRNA protocol miRNA_107_Sep09 (Agilent Technologies).
|
| Description |
miRNA profiling
|
| Data processing |
Tab-delimited text file were acquired and analyzed in R v3.1.3 software environment (www.r-project.org) using the limma package v (Smith 2005) of Bioconductor (www.bioconductor.org). Background was subtracted from signal for each detected spot (we used the value gBGSubSignal). Control type spots were removed. Undetected spots (i.e., those spots having a signal minus the background stricly smaller than zero) were removed. Probes with less than 5 of detected spots across all arrays in one of the two groups (ALK+ and ALK-) were removed from the analysis. Background corrected intensities of the remining spots after filtering (n=2491) were then log2-transformed and normalized for between-array comparison using quantile normalization (Bolstad et al.2003).
|
| |
|
| Submission date |
Jul 26, 2016 |
| Last update date |
Apr 30, 2017 |
| Contact name |
Sara Stigliani |
| E-mail(s) |
sara.stigliani@hsanmartino.it
|
| Organization name |
IRCCS AOU San Martino-IST
|
| Lab |
UOS Centro Fisiopatologia della Riproduzione Umana
|
| Street address |
largo R Benzi 10
|
| City |
Genova |
| ZIP/Postal code |
16132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL14943 |
| Series (2) |
| GSE84841 |
A genome-wide microRNA profiling indicates miR-424-5p and miR-503-5p as regulators of ALK expression in neuroblastoma (NB cell lines) |
| GSE86889 |
A genome-wide microRNA profiling indicates miR-424-5p and miR-503-5p as regulators of ALK expression in neuroblastoma |
|
