|
| Status |
Public on Jul 03, 2015 |
| Title |
ITD1 |
| Sample type |
genomic |
| |
|
| Source name |
FLT3-ITD AML patient sample
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: FLT3-ITD AML
|
| Growth protocol |
Patient and donor samples were obtained either from blood or bone marrow. Lymphoprep extraction of leukocytes was performed following 30 min no brake centrifugation. Enrichment for CD34 and CD117 were checked via FACS analysis. For CD14 samples, enricment for CD14 was controlled by FACS analysis. Where available, purification was performed using MACS columns following anti-CD34 bead conjugation to samples (anti-CD14 for CD14 samles).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Phenol-choroform
|
| Label |
Biotin, DNP
|
| Label protocol |
HumanMethylation 450K BeadChip
|
| |
|
| Hybridization protocol |
HumanMethylation 450K BeadChip
|
| Scan protocol |
HumanMethylation 450K BeadChip
|
| Data processing |
For the analysis of methylation sample data, image scanning, processing, feature extraction and normalization were performed in Illumina GenomeStudio. All intensities are combined in the TPS1928_SampleMethylationProfile_FinalReport_20Jun11_HL_NHL.txt file. Higher-level analysis was performed in R using IMA (https://www.rforge.net/IMA/index.html) followed by a custom R pipeline where probe methylation levels were aggregated per promoter. Promoter methylation fold changes were computed as log2 ratios
|
| |
|
| Submission date |
Jan 13, 2015 |
| Last update date |
Jul 03, 2015 |
| Contact name |
Pierre Daniel Cauchy |
| E-mail(s) |
cauchy@ie-freiburg.mpg.de
|
| Phone |
+49 (0)761 270-77576
|
| Organization name |
University Medical Center Freiburg
|
| Department |
Zentrum für Translationale Zellforschung
|
| Lab |
AG Onco-Immunology
|
| Street address |
Breisacher Str. 115
|
| City |
Freiburg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE64874 |
Chronic growth factor signaling in Acute Myeloid Leukemia is connected to a specific chromatin signature |
| GSE64934 |
Chronic growth factor signaling in Acute Myeloid Leukemia is connected to a specific chromatin signature [Methylation] |
|
