GSE130637
mRNA expression profiling in MDA-MB-231 (LM1) cells with a tet-incible MBD2 or p66a knock down, or treated with MBD2-targeting small molecule ABA or APC
The goal of this study is to compare mRNA expression profiles among wild type, MBD2 knock down, p66a knock down, and ABA- and APC-treated cells.. All cell lines were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. For the doxycycline inducible gene expression regulation, each cell lines were incubated in the presence of 1 µg/ml doxycycline for 2 days. For the drug treatment, MDA-MB-231 (LM1) cells were incubated in the presence of 10 µM ABA or APC for 2 days. Total cellular RNAs were extracted using Qiazol reagent. The RNA quality was examined by spectrophotometry, agarose gel electrophoresis (calculating the 18S and 28S rRNA ratio) and an Agilent Technologies 2100 Bioanalyzer (ensuring a RIN value greater than 7). Library was prepared with QuantSeq 3' mRNA-Seq Library Prep Kit FWD. The constructed libraries were subjected to 75-bp single-end sequencing using an Illumina NextSeq 500 sequencer. Using an optimized data analysis workflow, we mapped to the human genome (build hg19) and identified 25,737 transcripts in these cell lines. Overall design: Duplicated mRNA profiles of WT, tet-inducible MBD2 or p66a knock down, and ABA- or APC-treated MDA-MB-231 (LM1) cells are generated by quant-sequencing using Illumina Casava1.8.and then examine the expression patterns among these groups of cells.