|
| Status |
Public on Nov 23, 2011 |
| Title |
SJTALL038 |
| Sample type |
RNA |
| |
|
| Source name |
RNA extracted from diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia (non-ETP)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: tumor cells
|
| Growth protocol |
RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneTitan system.
|
| Description |
RNA extracted from tumor cells obtained at diagnosis
|
| Data processing |
Data were background adjusted, normalized and summarized by the RMA method. The Bioconductor package was used for this analysis.
|
| |
|
| Submission date |
Apr 19, 2011 |
| Last update date |
Dec 31, 2012 |
| Contact name |
Charles G Mullighan |
| E-mail(s) |
charles.mullighan@stjude.org
|
| Phone |
1-901-595-3387
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL13158 |
| Series (1) |
| GSE28703 |
Discovery of novel recurrent mutations and rearrangements in early T-cell precursor acute lymphoblastic leukemia by whole genome sequencing |
|
| Relations |
| Reanalyzed by |
GSM1058660 |
