patient sample type: Acute myeloid leukemia diagnostic sample cell type: mononuclear cells disease state: AML with complex karyotype
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated from the samples using the Trizol reagent (Invitrogen, Carlsbad, CA).
Label
biotin
Label protocol
0.2 microgram of total RNA was used for target preparation according to the manufacturer's protocol (GeneChip Whole Transcript Sense Target Labelling Assay manual, Affymetrix, Santa Clara, CA).
Hybridization protocol
The processed RNA was hybridized on GeneChip Human Exon 1.0 ST microarrays for 17 hours at 45oC and 60 rpm.
Scan protocol
The arrays were scanned using Affymetrix GeneChip® Scanner 3000.
Description
genome-wide analysis of alternative splicing in acute myeloid leukemia
Data processing
Probe set summarization, background correction and normalization was performed by applying the robust multiarray average (RMA) algorithm. The exon array data were analysed in (1) R, oneChannelGUI 1.10.7 (Sanges R. et al., 2010), (2) easyExon 1.0.4 (Chang T-Y et al., 2008), (3) Xray 3.9 (Biotique Systems, Reno, NV) and (4) GeneSpring 11.0 (Agilent Technologies, Palo Alto, CA). probe group file: HuEx-1_0-st-v2.r2.pgf meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
