|
| Status |
Public on Aug 01, 2010 |
| Title |
DS-AMKL01 |
| Sample type |
RNA |
| |
|
| Source name |
DS-AMKL sample 1, sorted blasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: megakaryocytic leukemia blasts
disease: Down Syndrome-AMKL
cell description: FACS sorted leukemic blasts from patients
|
| Treatment protocol |
N/A
|
| Growth protocol |
Cell lines were grown in RPMI1640+15%FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA followed by cleaning up using columns from the Promega SV total RNA isolation kit.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to U133 Plus 2.0 chips overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.
|
| Scan protocol |
Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.
|
| Description |
Gene expression data from sorted primary leukemic cells.
|
| Data processing |
The raw CEL files were imported into dChip and normalized with dChip. After normalization, the model-based expression values were calculated by dChip and exported.
|
| |
|
| Submission date |
Jun 17, 2009 |
| Last update date |
Jul 23, 2010 |
| Contact name |
Zhe Li |
| E-mail(s) |
li@bloodgroup.tch.harvard.edu
|
| Phone |
617-919-2052
|
| Organization name |
Children's Hospital Boston
|
| Department |
Division of Hematology/Oncology
|
| Lab |
Stuart Orkin's Lab
|
| Street address |
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE16655 |
Developmental stage-specific interplay between GATA1 and IGF signaling in fetal hematopoiesis and leukemogenesis |
| GSE16677 |
Gene expression profiling of Down Syndrome (DS)-AMKL and non-DS AMKL samples |
|
