NOMO1, KG1, PLB985, ML2, HL-60, EOL1, FKH1, GDM1, HNT34, THP1, SKM1, PL21, ME-1, KMOE-2, GF-D8, HEL, SET2, KG1?, KASUMI-1, MO7e and NB4 were grown in RPMI 1640 medium supplemented with 10% or 20% FBS; F-36P was cultured in RPMI 1640 medium supplemented with 10% FBS and 5ng/ml human IL-3; OCI-M1, OCI-M2, SHI-1, and SH-2 were cultured in IMDM medium supplemented with 20% FBS. OCI-AML2, OCI-AML5, OCI-AML3 were cultured in alpha-MEM medium supplemented with 10% or 20% FBS and GM-CSF or SCF. All cell lines were placed in a 37C humidified incubator containing 5% CO2. 10x10^6 cells were washed with 1xPBS and the cell pellets were stored at -80C before sending out for Microarray analysis.
Extracted molecule
total RNA
Extraction protocol
Total RNA is isolated using the Qiagen miRNeasy Mini Kit (Qiagen, #217004).
Label
Biotin
Label protocol
RNA samples are converted into labeled target antisense RNA (cRNA) using the Single-Round RNA Amplification and Biotin Labelling System (Enzo).
Hybridization protocol
cRNA is purified using magnetic beads and quantitated using spectrophotometry. Next, 11ug of purified cRNA is fragmented using a 5X Fragmentation buffer, then a hybridization cocktail is prepared and added to the fragmentation product using the Hybridization, Wash and Stain kit (Affymetrix), applied to Human U133_Plus2.0 arrays, and incubated at 45°C for 16 hours.
Scan protocol
Following hybridization, arrays are washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip Scanner
Description
Gene expression data from AML cell line
Data processing
Data extraction was performed using Expression Console
