|
| Status |
Public on Feb 28, 2017 |
| Title |
ALL_patient_153 [HG-U133_Plus_2] |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow mononuclear cells, Ph-positive ALL
|
| Organism |
Homo sapiens |
| Characteristics |
age: adult
cell type: bone marrow mononuclear cells
disease state: acute lymphoblastic leukemia (ALL)
all type: Ph-positive
|
| Treatment protocol |
Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute lymphoblastic leukemia (ALL).
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mononuclear cells from bone marrow (BM) 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 |
Sample name: BER_00136
|
| Data processing |
Data normalization was performed using the Robust Multichip Average (RMA) method as described by Irizarry et al. 2003. 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. Only the 44754 probe sets present both on the A, B chips and the 2.0 Plus chips were included in the analysis. Some probe sets on the A, B chips tend to have lower mean signal levels and higher standard deviations than the corresponding probe sets on the Plus 2.0 chips. To eliminate this batch effect resulting from the different chip designs, we performed a second normalization using an empirical Bayesian method.
|
| |
|
| Submission date |
Feb 17, 2015 |
| Last update date |
Nov 14, 2018 |
| Contact name |
Tobias Herold |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)
|
| Department |
Department of Internal Medicine III
|
| Street address |
Marchioninistr. 15
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE66002 |
Ph-like acute lymphoblastic leukemia in adults is characterized by IgH-CRFL2 and JAK2 mutations and poor prognosis [HG-U133_Plus_2] |
| GSE66006 |
Ph-like acute lymphoblastic leukemia in adults is characterized by IgH-CRFL2 and JAK2 mutations and poor prognosis |
|
| Relations |
| Reanalyzed by |
GSE122511 |
