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Sample GSM1309367 Query DataSets for GSM1309367
Status Public on Jul 31, 2014
Title Patient 12 in group SynSa2
Sample type genomic
 
Channel 1
Source name tumor sample
Organism Homo sapiens
Characteristics histosubtype: synovial sarcoma
age at diagnosis [years]: 39
gender: Female
Treatment protocol not applicable
Growth protocol not applicable
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from the frozen tumor specimens using High Pure PCR Template Preparation Kit (Roche).
Label Cy5
Label protocol 1ug of genomic DNA was labeled using Cy5 dye, and 1ug reference female DNA was labeled using Cy3 dye, according to manufacturer's recommendations. Male and female Megapool Reference DNA (catalog no. EA-100M and EA-100F) (KREATECH Diagnostics) were used for the aCGH experiments.
 
Channel 2
Source name Reference DNA
Organism Homo sapiens
Characteristics reference: Pooled genomic DNA from 100 healthy individuals
Treatment protocol not applicable
Growth protocol not applicable
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from the frozen tumor specimens using High Pure PCR Template Preparation Kit (Roche).
Label Cy3
Label protocol 1ug of genomic DNA was labeled using Cy5 dye, and 1ug reference female DNA was labeled using Cy3 dye, according to manufacturer's recommendations. Male and female Megapool Reference DNA (catalog no. EA-100M and EA-100F) (KREATECH Diagnostics) were used for the aCGH experiments.
 
 
Hybridization protocol Labeled samples were hybridized to SurePrint G3 Human CGH 4x180K whole-genome microarrays (G4449A) (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol.
Scan protocol The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, SantaClara, CA, USA).
Description aCGH profile in primary tumor sample
Data processing Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, SantaClara, CA, USA). aCGH data were analyzed using Agilent Genomic Workbench 7.0.4.0. software (Agilent Technologies, SantaClara, CA, USA). The ADM-2 algorithm was applied to identify DNA copy number aberrations (CNAs). Aberration Filter: ( Minimum Number of Probes for Amplification >= 500 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.25 ) OR ( Minimum Number of Probes for Deletion >= 500 AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.25 )
Normalized log2 ratio (Cy5/Cy3), ADM-2 alogrithm, threshold 6.0, calculated by the Agilent Genomic Workbench 7.0.4.0. software.
 
Submission date Jan 17, 2014
Last update date Jul 31, 2014
Contact name Joanna Przybyl
E-mail(s) jprzybyl@stanford.edu
Organization name Stanford University
Department Department of Pathology
Street address 300 Pasteur Drive
City Stanford
ZIP/Postal code 94305
Country USA
 
Platform ID GPL10123
Series (2)
GSE54183 Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features [aCGH]
GSE54188 Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features

Data table header descriptions
ID_REF
VALUE normalized log2 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 8.846538791e-003
2 0.000000000e+000
3 0.000000000e+000
4 -1.133763680e-001
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 4.191320979e-002
9 0.000000000e+000
10 0.000000000e+000
11 1.232117853e-001
12 0.000000000e+000
13 0.000000000e+000
14 0.000000000e+000
15 0.000000000e+000
16 0.000000000e+000
17 0.000000000e+000
18 0.000000000e+000
19 -6.548602164e-002
20 0.000000000e+000

Total number of rows: 180880

Table truncated, full table size 4205 Kbytes.




Supplementary file Size Download File type/resource
GSM1309367_aCGH_SynSa2_12.txt.gz 17.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file

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