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Sample GSM4315154 Query DataSets for GSM4315154
Status Public on Feb 15, 2020
Title neuroblastoma sample 162
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 GPL16237
Series (2)
GSE145339 19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis (Agilent-030587)
GSE145341 19p loss is significantly enriched in older age neuroblastoma patients and correlates with poor prognosis

Data table header descriptions
ID_REF
VALUE Values represent normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 0.1217238911
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0

Total number of rows: 180880

Table truncated, full table size 3529 Kbytes.




Supplementary file Size Download File type/resource
GSM4315154_162.txt.gz 19.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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