|
| Status |
Public on Apr 04, 2012 |
| Title |
leukemia-1 |
| Sample type |
RNA |
| |
|
| Source name |
AML-M3
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
age (yrs): 29
tissue source: bone marrow (BM)
disease state: acute myeloid leukemia (AML)
subtype: AML-M3
abnormality: t(15;17)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blasts and mononuclear cells were purified by use of NycoPrep 1.077A (Axis-Shield, Oslo, Norway) according to the manufacturer’s manual. RNA was isolated with the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix), and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were analyzed using the Affymetrix GeneChip Human Exon 1.0 ST Array (Affymetirx, Santa Clara, CA) according to the manufacturer's instructions.
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instructions (Affymetrix).
|
| Data processing |
After background correction according to the standard protocols, the quantified signals were normalized using Robust Multi-array Average (RMA), which is a robust algorithm of background-adjustment, quantile normalization, and log2-transformation. Partek Genomics Suite (Partek Inc., St. Louis, MI) was used for the analysis of the normalized data.
Exons included in analysis: core
Genome build: hg18
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Jun 28, 2011 |
| Last update date |
Apr 04, 2012 |
| Contact name |
chunjiang he |
| Organization name |
university of chicago
|
| Street address |
900 east 57th st
|
| City |
chicago |
| State/province |
il |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE30257 |
Identification of a common prognostic gene signature and its association with miR-181 regulation in human acute myeloid leukemia |
| GSE30285 |
Identification of prognostic gene signatures in AML |
|
