group: treatment perturbagen: Silybin cell line: breast cancer cell line MCF7 duration: 12 h
Treatment protocol
The MCF7 cells were treated by 102 molecules at 10μM or 1μM, DMSO, and 10μM mixture of four compounds (1:1:1:1) for 12h.
Growth protocol
The MCF7 cells were cultured in MEM/EBSS supplemented with 10% fetal bovine serum, 1mmol/L sodium pyruvate, 0.1mmol/L MEM non-essential amino acids, 100 unit/mL penicillin, and 100 mg/mL streptomycin in a incubator containing 5% CO2 at 37℃.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Label
biotin
Label protocol
Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Hybridization protocol
Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Scan protocol
Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)
Description
Gene expression data from human breast cancer cell line MCF7
Data processing
Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
