|
| Status |
Public on Dec 21, 2011 |
| Title |
UPN77_NK-AML_BM |
| Sample type |
RNA |
| |
|
| Source name |
NK-AML_Bone Marrow
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human acute myeloid leukemic cells
aml subtype: NK-AML
cell source: Bone Marrow
time point: Diagnosis
|
| Treatment protocol |
Blasts and mononuclear cells were purified by Ficoll-Hypaque density gradient centrifugation from bone marrow or peripheral blood samples (Nygaard, Oslo, Norway). Isolated cell samples were then immediately cryopreserved.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from 10e7 thawed cells using RNEasy® Mini Kits (Qiagen Incorporation, Valencia, USA). Total RNA quantification was performed using the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific Incorporation, Waltham, USA) according to manufacturer recommendations. Integrity of the extracted RNAs was assessed with the Bioanalyzer 2100 and the RNA6000 Nano kit (Agilent Technologies Incorporation, Santa Clara, USA).
|
| Label |
biotin
|
| Label protocol |
The Illumina Total Prep RNA Amplification Kit (Applied Biosystems / Ambion, Austin, USA) was used to generate biotinylated, amplified cRNA according to the manufacturer recommendations.
|
| |
|
| Hybridization protocol |
Hybridization on Illumina HumanHT-12 v3 Expression BeadChips and staining were performed according to Illumina’s protocol.
|
| Scan protocol |
Detection of cRNAs on microarrays using an I-Scan system were performed according to Illumina’s protocol.
|
| Data processing |
GenomeStudio 2010.3 software (Illumina Inc., San Diego, USA) and its Gene Expression Analysis Module (version 1.8.0) were used for signal extraction and normalization. The Invariant Rank normalization method was applied to the primary probe data. Processed probe data were then filtered according to the following criteria: minimal signal intensity fold change of 1.50 across all samples; minimal probe signal intensity absolute change of 150 across all samples; and maximal value for probe signal intensity of 50 000 across all samples.
|
| |
|
| Submission date |
Dec 20, 2011 |
| Last update date |
Dec 21, 2011 |
| Contact name |
Philippe Guardiola |
| E-mail(s) |
Phguardiol@aol.com
|
| Phone |
+33 2 41 35 44 82
|
| Fax |
+33 2 41 35 45 82
|
| Organization name |
Angers University Hospital
|
| Lab |
Plateforme SNP, Transcriptome & Epigenomique
|
| Street address |
4 rue Larrey
|
| City |
Angers |
| State/province |
Maine et Loire |
| ZIP/Postal code |
49000 |
| Country |
France |
| |
|
| Platform ID |
GPL6947 |
| Series (2) |
| GSE34577 |
Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples (training samples) |
| GSE34823 |
Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples |
|
