|
| Status |
Public on Nov 05, 2011 |
| Title |
L869 |
| Sample type |
RNA |
| |
|
| Source name |
Solitary chondrosarcoma grade II
|
| Organism |
Homo sapiens |
| Characteristics |
disease: solitary chondrosarcoma
tumor: chondrosarcoma grade II
idh1/2 mutations: yes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor samples were selected that contained more than 80% of tumor cells, as estimated on haematoxylin and eosin-stained frozen sections. RNA was isolated using TRIzol reagent (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit (Qiagen GmbH, Hilden, Germany) according to manufacturers instructions. RNA concentration was measured spectrophotometrically and the fragment sizes were determined using RNA 6000 Nano Labchip kit.
|
| Label |
biotin
|
| Label protocol |
As per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
As per manufacturer's instructions.
|
| Scan protocol |
As per manufacturer's instructions.
|
| Data processing |
For the expression array, unprocessed data were collected from BeadStudio and processed using variance-stabilizing transformation (vst) and robust spline normalization (rsn) with the Bioconductor package lumi. The processed data was analyzed using LIMMA (linear models for microarray data) analysis, which uses moderated t-test to detect differentially expressed genes between two groups by taking into account natural variance within these groups and correcting for multiple testing using false discovery rate indicating the number of differentially expressed genes between two groups.
Raw data file description: On the Illumina BeadChips, each sample is hybridized on 2 chips, which together compromise all probes per sample. There are four columns in each file. The first column represents the bead (there are approximately 30 replicate beads per probe on random positions on the Illumina BeadChip arrays, so the data that is generated is higly robust), the second the signal, and the other 2 the X and Y locations on the chip. These 2 raw files can be imported into BeadStudio, the program developed by Illumina for analyzing these data, or into R package beadarray.
|
| |
|
| Submission date |
Jul 21, 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 |
GPL6884 |
| Series (2) |
| GSE30835 |
mRNA expression data of tumor samples with/without IDH1/2 mutations and of controls |
| GSE30844 |
Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell haemangioma in Ollier disease and Maffucci syndrome |
|
