|
| Status |
Public on Jan 20, 2012 |
| Title |
medulloblastoma blood BL-2019 |
| Sample type |
genomic |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: 2019
gender: F
disease state: medulloblastoma
tissue: blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
High molecular weight genomic DNA was extracted from primary tissue and cell lines using either the standard SDS/Proteinase K method or Qiagen DNEasy Blood and Tissue Kits.
|
| Label |
biotin
|
| Label protocol |
As per instructions from manufacturer (Affymetrix).
|
| |
|
| Hybridization protocol |
As per instructions from manufacturer (Affymetrix).
|
| Scan protocol |
As per instructions from manufacturer (Affymetrix).
|
| Data processing |
CRMAv2 normalization using aroma.affymetrix. Probe signals were cablirated for crosstalk between allele probe pairs, normalized for nucleotide-position probe sequence effects, and summarized using the RmaCnPlm method (for the Mapping250K_Nsp platform) or the AvgCnPlm method for (the GenomeWideSNP_6 platform). Probe signals were then normalized for PCR fragment-length effects. Subsequently, raw copy-numbers were calcuated based on either the a pool of reference samples or pair-matched normals.
DNA copy-number values exported from aroma.affymetrix.
|
| |
|
| Submission date |
Dec 15, 2011 |
| Last update date |
Sep 12, 2014 |
| Contact name |
David J. H. Shih |
| E-mail(s) |
david.shih@utoronto.ca
|
| Phone |
(416) 813-7654
|
| Organization name |
Hospital for Sick Children
|
| Department |
Developmental and Stem Cell Biology
|
| Lab |
Peter Gilgan Centre for Research and Learning
|
| Street address |
686 Bay St
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE34258 |
Genome sequencing of childhood medulloblastoma brain tumors links chromothripsis with TP53 mutations |
|
