|
| Status |
Public on Dec 31, 2009 |
| Title |
CN_AML Patient 16: Wildtype CEBPA |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow mononuclear cells: AML, normal karyotype
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone-marrow mononuclear cells from CN-AML patient
genotype: Wildtype CEBPA
|
| Treatment protocol |
Pretreatment bone marrow or peripheral blood mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML) with a normal karyotype
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mononuclear cells from bone marrow (BM) or peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and in vitro transcription were performed according to standard Affymetrix protocols.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols
|
| |
|
| Hybridization protocol |
Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols
|
| Scan protocol |
Samples were scanned using an Affymetrix GeneChip scanner
|
| Description |
CN_AML Patient 16
|
| Data processing |
Normalization was performed using the variance stabilizing normalization algorithm. Custom chip definition files based on the GeneAnnot database were used for probe-set summarization, and probe set expression values were calculated by the median polish method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization.
|
| |
|
| Submission date |
Mar 12, 2009 |
| Last update date |
Mar 12, 2009 |
| Contact name |
Klaus H Metzeler |
| E-mail(s) |
klaus.metzeler@med.uni-muenchen.de
|
| Organization name |
University of Munich
|
| Department |
Department of Internal Medicine III
|
| Lab |
Laboratory for Leukemia Diagnostics
|
| Street address |
Marchioninistr. 15
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL8289 |
| Series (1) |
| GSE15210 |
Gene expression profiles of mono- and biallelic CEBPA mutations in cytogenetically normal AML |
|
