|
| Status |
Public on Aug 22, 2010 |
| Title |
AML sample 188 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
pooled AML blasts
|
| Organism |
Homo sapiens |
| Characteristics |
batch: 2nd batch
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted and sonicated to an average DNA length of 500 bp.
|
| Label |
Cy5
|
| Label protocol |
DNA was amplified in 2 steps, including a T7 sequenase extension using random primer with a fixed sequence linker and a second step of amplification using the fixed sequence primer and Taq polymerase. The products were purified and labeled with amino-allyl-conjugated dUTP using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) and random primer. Products were purified and crosslinked with monofunctional NHS-ester Cy3 or Cy5 dye.
|
| |
|
| Channel 2 |
| Source name |
AML blasts
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: AML
age: 57
gender: male
batch: 2nd batch
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
will update
|
| Label |
Cy3
|
| Label protocol |
DNA was amplified in 2 steps, including a T7 sequenase extension using random primer with a fixed sequence linker and a second step of amplification using the fixed sequence primer and Taq polymerase. The products were purified and labeled with amino-allyl-conjugated dUTP using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) and random primer. Products were purified and crosslinked with monofunctional NHS-ester Cy3 or Cy5 dye.
|
| |
|
| |
| Hybridization protocol |
Hybridizations were performed for 18h.
|
| Scan protocol |
Slides were scanned using an Axon 4000B scanner. Images were quantified using the SpotReader software.
|
| Description |
188-AML
|
| Data processing |
Background intensities given by the SpotReader software were subtracted from foreground intensities. The vsn method (W. Huber et al.; Bioinformatics 2002;18 Suppl 1:S96-104) was then applied separately to each batch of arrays for single color normalization of the green (ChIP) channel across all arrays within that dataset. A model with 48 strata per array according to the print-tips was used. Probes that were flagged by the Spotreader software in more than 25% of the samples as well as empty/blank probes were excluded from the estimation of the model’s parameters. The quantile that is used for the least trimmed sum of squares regression was set to 0.75. After parameter estimation, vsn transformation was applied to all probes. All computations were done within the R-package vsn (ver. 3.6.0).
|
| |
|
| Submission date |
Feb 22, 2010 |
| Last update date |
Aug 22, 2010 |
| Contact name |
Hans-Ulrich Klein |
| E-mail(s) |
h.klein@uni-muenster.de
|
| Organization name |
Columbia University Medical Center
|
| Department |
Neurology
|
| Lab |
Center for Translational and Computational Neuroimmunology
|
| Street address |
622 W 168th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL10087 |
| Series (1) |
| GSE20452 |
Profiling of H3K9me3 levels predicts Transcription Factor Activity and Survival in Acute Myeloid Leukemia |
|
