|
| Status |
Public on Mar 09, 2021 |
| Title |
glioma sample;IDHwt_GIII_3 |
| Sample type |
genomic |
| |
|
| Source name |
DNA from Glioma sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: glioma
gliomas classification (grade): Grade IIII
gliomas classification: IDH statut: IDHwt
|
| Growth protocol |
Immediately after surgery, glioma samples were snap-frozen and stored in liquid nitrogen. non-tumoral control brain samples were cadaveric specimens removed by autopsy 4-16 h following accidental death (Brain and Tissue Bank of Maryland).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were isolated from frozen tissue samples using the QIAamp DNA Mini Kit (Qiagen, Hamburg, GmbH)
|
| Label |
biotin
|
| Label protocol |
DNA and array processing were performed by the Genomic Platform/ Curie Institute (France) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
DNA and array processing were performed by the Genomic Platform/ Curie Institute (France) according to the manufacturer's protocol.
|
| Scan protocol |
Arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.
|
| Data processing |
Scanned data files were analyzed with Affymetrix Chromosome Analysis Suite v3.1 (ChAS) (Affymetrix Inc., USA) using the CytoScanHD_Array.na33.annot.db annotation file on hg19 genome. To find copy numbers variations, single sample analysis strategy were done using the reference model file “CytoScanHD_Array.na33.r2.REF_MODEL”. To prevent false positive CNVs detection arising due to inherent microarray “noise”, only alterations that involved at least 50 consecutive probes and spanning more than 100 kbp were considered in the analysis.
The file CNV_SSA_Results.txt contains a matrix of CNV fragments from single sample analyses
|
| |
|
| Submission date |
Nov 11, 2020 |
| Last update date |
Mar 09, 2021 |
| Contact name |
franck court |
| Organization name |
GReD CNRS
|
| Street address |
28 Place Henri Dunant
|
| City |
Clermont-Ferrand |
| ZIP/Postal code |
63000 |
| Country |
France |
| |
|
| Platform ID |
GPL16131 |
| Series (1) |
| GSE161275 |
CNV analysis of normal brain and glioma samples II |
|
