|
| Status |
Public on Jul 03, 2013 |
| Title |
sample 6_PAD_00427 |
| Sample type |
RNA |
| |
|
| Source name |
White blood human cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease: pediatric acute leukemia
groups: otherHOXA
mrd: Standard Risk
data analysis protocol: MILE2
|
| Treatment protocol |
White blood cells were isolated by density gradient centrifugation (Biocoll separating solution, Biochrome AG, Berlin, Germany).
|
| 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
|
| 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 |
MILE1, MILE2 and ES are small variants of the Affymetrix workup protocol and we used a method to remove batch effects.
Gene expression data from pediatric acute leukemia samples at diagnosis
|
| Data processing |
Expression data were analyzed using R software [v.2.14, www.r-ptoject.org] with BioConductor package [v.2.10, www.bioconductor.org].
Batch effects due to different protocols were removed from the data: ES is the standard affymetrix protocol following manufacturer instructions; MILE1 and MILE2 work-up protocols are described in J.Clin.Oncol (2010) 28(15): 2529-37.
|
| |
|
| Submission date |
Dec 06, 2012 |
| Last update date |
Jul 03, 2013 |
| Contact name |
Andrea Zangrando |
| E-mail(s) |
andrea.zangrando@unipd.it
|
| 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) |
| GSE42765 |
MLLT10 gene recombinations in pediatric T-Acute Lymphoblastic Leukemia |
|
