7 protocols
AccessionNameType
P-GSE27980-1
bioassay_data_transformation
ID_REF = VALUE = log2 normalized signal intensity
P-GSE27980-6
image_aquisition
according to the instruction manual, as described in the Affymetrix website
P-GSE27980-5
hybridization
according to the instruction manual, as described in the Affymetrix website
P-GSE27980-7
feature_extraction
Onlyl gene-level analyses was performed. RMA normalization, summarization by mean and batch effect removal, all were done by Partek Genomics suite (version 6.5) Copyright © 2010). Log2 signal intensities after normalization, summarization and batch effect removal, as implicated in the data processing raw. Only 17881 probes remain after sumarization.
P-GSE27980-4
labeling
according to the instruction manual, as described in the Affymetrix website
P-GSE27980-2
grow
Cells were grown in RPMI-1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mmol/ml L-glutamine, 0.01 M HEPES buffered saline, 100 units/ml penicillin, 0.1 mg/ml streptomycin, and 12.5 units/ml nystatin. All cells were routinely cultured in humidified air with 5% CO2 at 37°C. The cells were routinely tested for the presence of mycoplasma.
P-GSE27980-3
nucleic_acid_extraction
total RNA was isolated using the Qiagen Rneasy Mini Kit (Qiagen, Valencia, CA). Samples were treated for DNase using DNase Set (Qiagen). RNA concentrations were determined by the absorbance at 260 nm and quality control standards were A260/A280 = 1.8 – 2.0.