|
| Status |
Public on Nov 15, 2007 |
| Title |
Germ Cell Tumor 526A |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Genomic DNA from germ cell tumor 526A labeled with Cy3
|
| Organism |
Homo sapiens |
| Characteristics |
germ cell tumor
Histology: Ter(M)
Site: Sm Bowel & mesentery
|
| 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 |
|
