|
| Status |
Public on May 31, 2007 |
| Title |
PAD_00331_sample 4_preparation A |
| Sample type |
RNA |
| |
|
| Source name |
White blood human cells
|
| Organism |
Homo sapiens |
| Characteristics |
Leukemia samples
Bone Marrow sample
|
| Treatment protocol |
White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation (for ALL samples) or through hemolysis (for AML samples)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns (method A); Trizol extraction of total RNA was performed according to the manufacturer's instructions (method B); Trizol extraction of total RNA followed by purification step was performed according to the manufacturer's instructions (method C).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
|
| Scan protocol |
GeneChips were scanned using the Scan GCS3000Dx.
|
| Description |
Gene expression data from pediatric acute leukemia samples at diagnosis
Patient 4
ALL with t(12;21)
|
| Data processing |
The data were analyzed using R software [www.r-project.org] with BioConductor package [www.bioconductor.org] and Partek Genomics Suite software [www.partek.com].
|
| |
|
| Submission date |
May 08, 2007 |
| Last update date |
Nov 14, 2018 |
| Contact name |
Andrea Zangrando |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Padova
|
| Department |
Woman and Child's Health
|
| Lab |
Hemato-Oncology
|
| Street address |
Via Giustiniani, 3
|
| City |
Padova |
| ZIP/Postal code |
35138 |
| Country |
Italy |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE7757 |
Robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures. |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
| Reanalyzed by |
GSE122511 |
