|
| Status |
Public on Jul 19, 2011 |
| Title |
Maffucci Chondrosarcoma II |
| Sample type |
genomic |
| |
|
| Source name |
Maffucci Chondrosarcoma II (L2102)
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Maffucci
tumor: chondrosarcoma II
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from fresh frozen tissue was isolated using the wizard genomic DNA purification kit (Promega, Madison, WI), according to the manufacturer instructions.
|
| Label |
biotin
|
| Label protocol |
According to Affymetrix SNP 6.0 standard protocol
|
| |
|
| Hybridization protocol |
According to Affymetrix SNP 6.0 standard protocol
|
| Scan protocol |
According to Affymetrix SNP 6.0 standard protocol
|
| Data processing |
Genotyping was performed using the CRLMM algorithm in the Oligo package (Lin, 2008), copy number analysis using the aroma affymetrix package (Bengtsson, 2009), and we constructed LAIR plots to visualize regions of LOH and allelic imbalance (Corver, 2008) in R software (version 2.8). We have used CNCHP log ratio file as an input in Nexus (BioDiscovery, USA) software (version 4.1) and performed HMM based SNP-FASST segmentation for copy number analysis.
|
| |
|
| Submission date |
Jan 18, 2011 |
| Last update date |
Jul 19, 2011 |
| Contact name |
Twinkal Chandubhai Pansuriya |
| E-mail(s) |
t.c.pansuriya@lumc.nl
|
| Phone |
0031715266528
|
| Organization name |
LUMC
|
| Department |
Pathology
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
|
