|
| Status |
Public on Feb 15, 2020 |
| Title |
neuroblastoma sample 123 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
neuroblastoma tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neuroblastoma tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from frozen neuroblastoma primary tumors was extracted using the QiaAmp DNA MINI kit (Qiagen). Its quality was assessed by agarose gel electrophoresis. Tumor samples were obtained before treatment at the time of diagnosis
|
| Label |
Cy5
|
| Label protocol |
Genomic DNA was labeled following Agilent protocol (G4410-90010_CGH_Enzymatic_Protocol_v6.2.1). Yield was assessed with a nanodrop system. Tumor DNA was labeled with cyanine-5 (Cy5), and reference DNA (Agilent's Human Reference DNA) was labeled with cyanine-3 (Cy3).
|
| |
|
| Channel 2 |
| Source name |
Agilent Human Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Agilent Human Reference DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from frozen neuroblastoma primary tumors was extracted using the QiaAmp DNA MINI kit (Qiagen). Its quality was assessed by agarose gel electrophoresis. Tumor samples were obtained before treatment at the time of diagnosis
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA was labeled following Agilent protocol (G4410-90010_CGH_Enzymatic_Protocol_v6.2.1). Yield was assessed with a nanodrop system. Tumor DNA was labeled with cyanine-5 (Cy5), and reference DNA (Agilent's Human Reference DNA) was labeled with cyanine-3 (Cy3).
|
| |
|
| |
| Hybridization protocol |
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol
|
| Scan protocol |
Arrays were scanned using an Agilent Technologies Scanner G2505C, each hybridization produced a pair of 16-bit images, which were processed using the Agilent Feature Extraction 10.5 Software
|
| Data processing |
The data were analyzed using the Agilent Genomic Workbench 7.0.40 software, the altered chromosomal regions and breakpoints events were detected using ADM-1 (threshold 10) with 0.5 Mb window size. Losses were defined as loci with log2 ratio ≤-0.5, gain as loci with log2 ratio ≥0.5, amplifications as loci with log2 ratio ≥2 and loci with log2 ratio ≥3.5 were considered as high level of amplifications.
|
| |
|
| Submission date |
Feb 14, 2020 |
| Last update date |
Feb 15, 2020 |
| Contact name |
Annalisa Pezzolo |
| E-mail(s) |
annalisapezzolo@gaslini.org
|
| Organization name |
IRCCS Istituto Gaslini
|
| Lab |
Laboratorio Cellule Staminali e Terapie Cellulari
|
| Street address |
Via Gerolamo Gaslini, 3
|
| City |
Genova |
| ZIP/Postal code |
16147 |
| Country |
Italy |
| |
|
| Platform ID |
GPL2879 |
| Series (2) |
| GSE145337 |
19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis (Agilent-013282, dataset 2) |
| GSE145341 |
19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis |
|
