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Sample GSM685399 Query DataSets for GSM685399
Status Public on Jul 01, 2011
Title Cribriform nevroepithelial tumor
Sample type genomic
 
Channel 1
Source name Human brain
Organism Homo sapiens
Characteristics gender: Female
tumor type: Cribriform nevroepithelial
Growth protocol Fresh-frozen
Extracted molecule genomic DNA
Extraction protocol Mag-Attract DNA Mini M48 kit (QIAGEN, Hilden, Germany)
Label Cy3
Label protocol The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.
 
Channel 2
Source name Control_DNA_Promega
Organism Homo sapiens
Characteristics sample type: reference
gender: Female
Growth protocol Fresh-frozen
Extracted molecule genomic DNA
Extraction protocol Mag-Attract DNA Mini M48 kit (QIAGEN, Hilden, Germany)
Label Cy5
Label protocol The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.
 
 
Hybridization protocol The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.
Scan protocol All slides were scanned with the Agilent DNA Microarray Scanner with Surescan High-Resolution technology and data extracted using the Agilent Feature Extraction Software v. 10.5.1.1 as described in the Agilent Oligo aCGH protocol.
Data processing Agilent Feature Extraction Software (version 10.5.1.1) and Genomic Workbench software (Agilent Technologies Inc., Palo Alto, California, USA). Aberrant DNA copy number intervals identified using the Aberration Detection Method 2 (ADM-2), default threshold setting 6.0, and Fuzzy Zero correction algorithm applied. To ensure the exclusion of very low or very small aberrations, we added a custom-made aberration filter defining a region with a copy number aberration as a region with minimum five probes gained/lost and with minimum absolute average log2 ratio of 0.2 (gain) or -0.2 (loss). A loss defined as homozygous when the log2 ratio was lower than -1, and a gain was regarded as high level amplification when the log2 ratio was higher than 1.
 
Submission date Mar 03, 2011
Last update date Jul 01, 2011
Contact name Hanne-Sofie S Dahlback
E-mail(s) h.s.s.dahlback@medisin.uio.no
Organization name The Norwegian Radium Hospital
Department Section for Cancer Cytogenetics
Street address Montebello
City Oslo
ZIP/Postal code 0310
Country Norway
 
Platform ID GPL10123
Series (1)
GSE27671 Genomic Aberrations in Paediatric Gliomas and Embryonal Tumours

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy3/Cy5 (test/reference)
INV_VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE INV_VALUE
1 -0.0552465 5.524649445e-002
2 0.000000000e+000 0.000000000e+000
3 -0.0872907 8.729069268e-002
4 0.000000000e+000 0.000000000e+000
5 0.000000000e+000 0.000000000e+000
6 0.000000000e+000 0.000000000e+000
7 -0.269706 2.697057563e-001
8 0.000000000e+000 0.000000000e+000
9 0.0519146 -5.191460585e-002
10 0.000000000e+000 0.000000000e+000
11 0.000000000e+000 0.000000000e+000
12 -0.0517853 5.178533044e-002
13 0.236448 -2.364483440e-001
14 0.000000000e+000 0.000000000e+000
15 0.000000000e+000 0.000000000e+000
16 0.000000000e+000 0.000000000e+000
17 0.000000000e+000 0.000000000e+000
18 0.000000000e+000 0.000000000e+000
19 0.000000000e+000 0.000000000e+000
20 0.000000000e+000 0.000000000e+000

Total number of rows: 180880

Table truncated, full table size 6066 Kbytes.




Supplementary file Size Download File type/resource
GSM685399.txt.gz 50.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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