Opti-MEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution
Extracted molecule
total RNA
Extraction protocol
Total RNA extraction using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol. Extracted RNA was treated with RNAse Free DNAse kit to remove traces of geomic DNA prior to analysis
Label
biotin
Label protocol
Biotin
Hybridization protocol
Affymetrix GeneChip® WT Plus Reagent Kit (ThermoFisher, Santa Clara, CA) was used for the preparation of samples and generation of ss-cDNA for hybridization250 ng of total RNA were used for input. All the reactions and hybridizations were carried out according to the manufacturer's protocol. Affymetrix GeneChip Human Gene 2.0 ST Array were washed using the GeneChip® Fludics Station 450
Scan protocol
GeneChip Scanner 3000
Data processing
The raw data was first processed with R package oligo (Carvalho BS, Irizarry RA (2010). “A Framework for Oligonucleotide Microarray Preprocessing.” Bioinformatics, 26 (19), 2363-7. ISSN 1367-4803, doi: 10.1093/bioinformatics/btq431) and then normalized with RMA (Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4):e15. doi:10.1093/nar/gng015).
Expression Data from YUGEN8 parental cell line and its clonally related isogenic variants Clone 1A, Clone 2A, and Clone 2B hereby labeled as GEN, Cl.1A, Cl.2A, and Cl.2B respectively
