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Sample GSM213584 Query DataSets for GSM213584
Status Public on Nov 15, 2007
Title Germ Cell Tumor 399A
Sample type genomic
 
Channel 1
Source name Genomic DNA from germ cell tumor 399A labeled with Cy3
Organism Homo sapiens
Characteristics germ cell tumor
Histology: EC
Site: testis
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using previously described protocols (see Chen W. et al., Blood 107(6):2477-85, 2006)
Label Cy5
Label protocol DPNII digested DNA was labeled using a Bioprime Labeling Kit (Invitrogen) incorporating fluorescent dye (either dCTP-Cy3 or dCTP-Cy5) and mixed with differentially labeled reference DNA
 
Channel 2
Source name placenta reference DNA
Organism Homo sapiens
Characteristics karyotypically normal female placental DNA
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using previously described protocols (see Chen W. et al., Blood 107(6):2477-85, 2006)
Label Cy3
Label protocol DPNII digested DNA was labeled using a Bioprime Labeling Kit (Invitrogen) incorporating fluorescent dye (either dCTP-Cy3 or dCTP-Cy5) and mixed with differentially labeled reference DNA
 
 
Hybridization protocol Labeled test and reference DNA were mixed and hybridized overnight in Spectral Hybridization buffer (Spectral Genomics) at 37C under lifter slips (Erie Scientific); following morning slides were washed sequentially according to array manufacturer's recommendations (Spectral Genomics)
Scan protocol Slides were scanned on an Axon 4000B scanner
Images were quantified using Genepix Pro v.3
Description abbreviations: EC- embryonal carcinoma; CC- choriocarcinoma; Sem- Seminoma; YST- yolk sac tumor; Ter- teratoma; Ter(I)- immature teratoma; Ter(M)- mature teratoma; TMT- teratoma with malignant transfomation; trophs- trophoblast cells; rplnd- retroperitoneal lymph node; LN- lymph node
Data processing Utilized difference between log2 median Cy3 and Cy5 values as raw data for analysis; Subarray (block) median normalization and global loess correction was performed and duplicates were averaged; Changes in copy number were identified by CBS algorithm (see Chen W. et al., Blood 107(6):2477-85, 2006)
 
Submission date Jul 27, 2007
Last update date Aug 14, 2011
Contact name James Korkola
E-mail(s) [email protected]
Phone 212-639-8281
Organization name Memorial Sloan-Kettering
Department Cell Biology
Lab Chaganti
Street address 1275 York Ave
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL5679
Series (1)
GSE8614 Genomic Profiling of Adult Male Germ Cell Tumors

Data table header descriptions
ID_REF
VALUE normalized log2 ratio [(Cy3/Cy5) or (Cy5/Cy3)]

Data table
ID_REF VALUE
RP1-62I8 -0.046631664
RP11-421C4 -0.032681319
RP1-283E3 -0.086657458
RP1-163G9 -0.108649545
CTC-232B23 -0.032413238
RP11-447M5 -0.013768162
RP4-703E10 -0.008811511
RP3-491M17 0.014531136
RP11-33M12 -0.043169232
RP3-438L4 0.013208615
RP4-633I8 0.015006017
RP11-476D13 -0.114508937
AL031984.13 -0.064191657
RP3-330O12 0.020854618
RP5-888M10 -0.154918867
RP11-219C24 0.085880955
RP4-726F20 -0.010056979
RP5-864I18 -0.01582218
RP11-169K16 -0.050799455
RP1-163M9 0.332342781

Total number of rows: 2593

Table truncated, full table size 55 Kbytes.




Supplementary file Size Download File type/resource
GSM213584.gpr.gz 523.8 Kb (ftp)(http) GPR
Processed data included within Sample table

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