|
| Status |
Public on Jun 20, 2012 |
| Title |
Adherent_1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ESFT adherent cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary Ewing’s sarcoma family tumor (ESFT)
spheres/adherent: adherent
|
| Growth protocol |
Primary ESFT spheres were cultured in IMDM (Gibco), supplemented with 20% KO serum (Gibco), pen/strep (Gibco), 10 ug/ml LIF (Millipore), 10 ng/mL of recombinant human epidermal growth factor (Invitrogen), 10 ng/mL of recombinant human basic fibroblast growth factor (Invitrogen). Adherent cells were derived from spheres and cultured in IMDM, 10% FCS and pen/strep for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trifast (Peqlab) according to the manufacturer’s recommendations.
|
| Label |
Hy3
|
| Label protocol |
Total RNA from sample and reference was labelled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
Human Universal Reference RNA from Ambion
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Growth protocol |
Primary ESFT spheres were cultured in IMDM (Gibco), supplemented with 20% KO serum (Gibco), pen/strep (Gibco), 10 ug/ml LIF (Millipore), 10 ng/mL of recombinant human epidermal growth factor (Invitrogen), 10 ng/mL of recombinant human basic fibroblast growth factor (Invitrogen). Adherent cells were derived from spheres and cultured in IMDM, 10% FCS and pen/strep for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trifast (Peqlab) according to the manufacturer’s recommendations.
|
| Label |
Hy5
|
| Label protocol |
Total RNA from sample and reference was labelled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| |
| Hybridization protocol |
The hybridization was performed according to the miRCURY LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
|
| Scan protocol |
The miRCURY LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA).
|
| Description |
Hy3: 1_Exiqon_14173989_S01.txt
Hy5: 0_Exiqon_14173989_S01.txt
|
| Data processing |
Image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm in Bioconductor.
|
| |
|
| Submission date |
Aug 02, 2011 |
| Last update date |
Jun 22, 2012 |
| Contact name |
Paolo Provero |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Turin
|
| Department |
Molecular Biotechnology and Health Sciences
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| ZIP/Postal code |
I-10100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11432 |
| Series (2) |
| GSE31145 |
MicroRNA expression profiling of Ewing sarcoma spheres vs. adherent cells |
| GSE31146 |
A TARBP2-dependent miRNA expression profile determines cancer stem cell properties and provides new candidate therapeutic reagents in Ewing's sarcoma |
|
