|
| Status |
Public on Jun 21, 2016 |
| Title |
Primary AML patient 82 |
| Sample type |
RNA |
| |
|
| Source name |
AML BM
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone Marrow
fab: M2
c/ebpsigma quartile: Q1
karyotypic aberration: t(6;9) DEK/NUP214
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total bone marrow RNA was extracted using TRIzol reagent (Invitrogen) according to manufacturer guidelines, quantified using UV spectroscopy (Nanodrop Technologies), and qualitatively assessed using an Agilent2100 Bioanalyzer (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.
|
| |
|
| Hybridization protocol |
Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.
|
| Scan protocol |
The Genechips were scanned with an Affymetrix 7G scanner according to manifacturer guidelines.
|
| Description |
Gene expression data from pediatric AML patient according to C/EBPδ expression level (gene-level)
|
| Data processing |
The CEL files generated were analyzed through Affymetrix Expression Console Software (version 1.3) which normalizes array signals using a robust multiarray averaging (RMA) algorithm. Normalized data were analyzed using Transcriptome Analysis Console (TAC) 3.0 Software (Affymetrix). An unpaired t-test was applied to identify differentially expressed transcript genes between sample pairs and probes with P-values less than 0.01 and fold-change >2 were declared significant.
|
| |
|
| Submission date |
Nov 29, 2015 |
| Last update date |
Jun 21, 2016 |
| Contact name |
Matteo Zampini |
| E-mail(s) |
m.zampini@irpcds.org
|
| Phone |
+390498211466
|
| Organization name |
Istituto di Ricerca Pediatrica (IRP) Città della Speranza
|
| Street address |
corso stati uniti 4
|
| City |
Padova |
| State/province |
PD |
| ZIP/Postal code |
35127 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE75461 |
Pediatric AML classification according to C/EBPδ expression |
|
