|
| Status |
Public on Jul 19, 2011 |
| Title |
L2195N |
| Sample type |
genomic |
| |
|
| Source name |
Maffucci patient normal (fresh frozen)
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Maffucci
tissue: fresh frozen normal
sample type: control
|
| 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 |
GeneChip GSC3000 7G Whole-Genome Association System. According to Affymetrix SNP 6.0 standard protocol.
|
| Description |
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. Copy number inferred after correction with the 5 closest normals.
|
| |
|
| Submission date |
Jul 16, 2010 |
| 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 (4)
|
| GSE22965 |
Genome-wide analysis of Ollier disease: Is it all in the genes? |
| GSE22984 |
Affymetrix SNP6.0 on Ollier disease-related tumors |
| GSE26674 |
SNP array analysis on Maffucci tumours |
|
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