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Sample GSM1062714 Query DataSets for GSM1062714
Status Public on Jan 01, 2014
Title A (TUMOUR)
Sample type genomic
 
Source name Tumour
Organism Homo sapiens
Characteristics cell type: Neuroblastoma
gender: Male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from blood was extracted from lymphocytes of peripheral blood at diagnosis using the Qiagen DNA Blood Mini Kit. Genomic DNA from tumour was extracted from tissue of pieces of neuroblastoma tumour at diagnosis using the Qiagen DNA Blood Mini Kit, as well. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Data processing Analysis were performed using Affymetrix® Chromosome Analysis Suite (ChAS) software. Gains and losses in tumour and blood samples from each patient were estimated with 95% confidence intervals. Map position was based on the UCSC Genome Browser, February 2009, gh19 (NCBI Build 37 reference sequence).
 
Submission date Jan 11, 2013
Last update date Jan 01, 2014
Contact name Tatiana Vaz de Carvalho
E-mail(s) tatianacarvalho_inca@yahoo.com.br
Organization name INCA
Department Genetica
Lab Genetica
Street address Andre Cavalcanti 37
City Rio de Janeiro
State/province Rio de Janeiro
ZIP/Postal code 20231-050
Country Brazil
 
Platform ID GPL11157
Series (1)
GSE43454 Copy Number Variation in Neuroblastoma

Data table header descriptions
ID_REF
VALUE LOG2 RATIO
WEIGHTED LOG2 RATIO
SMOOTH SIGNAL

Data table
ID_REF VALUE WEIGHTED LOG2 RATIO SMOOTH SIGNAL
C-0HT3C -0.373600 -0.106168 1.951031
C-0HT3D -0.511715 -0.106168 1.950641
C-0HT3E 0.787255 -0.106168 1.950157
C-0HT3F -0.106168 0.313595 1.949998
C-0HT3I 0.523380 0.313595 1.951006
C-0HT48 0.313595 0.313595 1.951712
C-0HT4C 0.092701 0.313595 1.953035
S-2K62M 0.494536 0.092701 1.953322
C-0HT4G -0.657424 0.092701 1.954630
C-0HT4K -0.187392 0.226100 1.953578
C-0HT4L 0.226100 -0.033704 1.954376
C-0HT4M 0.523419 -0.032999 1.954997
C-0HT4O -0.033704 -0.032999 1.955480
C-0HT4P -0.032999 -0.033704 1.955506
C-0HT4R -0.419423 -0.188899 1.955668
S-2H4KY -0.188899 -0.419423 1.956562
C-0HT4U -0.460742 -0.433115 1.956984
S-2K3DK -0.491383 -0.438448 1.957069
C-0HT4X -0.433115 -0.438448 1.957331
S-2KEV0 -0.438448 -0.433115 1.957844

Total number of rows: 2141868

Table truncated, full table size 74178 Kbytes.




Supplementary file Size Download File type/resource
GSM1062714_A_TUMOUR.CEL.gz 21.0 Mb (ftp)(http) CEL
GSM1062714_A_TUMOUR.cy2wg.cychp.gz 36.8 Mb (ftp)(http) CYCHP
Processed data included within Sample table
Processed data provided as supplementary file

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