|
| Status |
Public on Nov 05, 2011 |
| Title |
L1829 |
| Sample type |
genomic |
| |
|
| Source name |
Solitary enchondroma
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age: 13
tumor: Solitary enchondroma
genotype/variation: with IDH1 mutation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from frozen tumors containing at least 80% of tumors cells, as estimated on haematoxylin using the Wizard Genomic DNA Purification Kit (Promega,Madison, WI), according to the manufacturer’s instructions.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
Bisulfite treatment was performed using EZ DNA Methylation™ Kit (Zymo
Research, Orange, CA)using 1ug of genomic DNA . Bisulphite converted DNA was then hybridized to Illumina HumanMethylation27 BeadChip (Illumina Inc., San Diego, CA) by following
manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
According to manufacturer’s protocol
|
| Scan protocol |
According to manufacturer’s protocol
|
| Data processing |
Infinium Unsupervised clustering analysis was performed
25 using the Ward’s clustering algorithm based on Euclidian distance. The 2000 most variable CpG sites (excluding those on the X and Y chromosomes) were used in theclustering analysis.
|
| |
|
| Submission date |
Aug 11, 2011 |
| Last update date |
Nov 05, 2011 |
| Contact name |
Twinkal Chandubhai Pansuriya |
| E-mail(s) |
[email protected]
|
| 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 |
GPL8490 |
| Series (2) |
| GSE30844 |
Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell haemangioma in Ollier disease and Maffucci syndrome |
| GSE31337 |
Methylation profiling of enchondromas with and without IDH1 mutations |
|
