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Genome-wide analysis of mRNA expression profile in MDA-MB-231 cells treated with or without 3.75 μM DCC-2036 for 48 hours.

ABSTRACT: Genome-wide analysis of mRNA expression profile in MDA-MB-231 cells treated with or without 3.75 μM DCC-2036 for 48 hours.

PROVIDER: PRJNA430226 | ENA |

REPOSITORIES: ENA

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Genome-wide analysis of mRNA expression profile in MDA-MB-231 cells treated with or without 3.75 μM DCC-2036 for 48 hours.

Project description:Our study found that DCC-2036, the novel tyrosine kinase inhibitor, has potent activity against triple negative breast cancer (TNBC). To better understand the molecular mechanisms involving in the effect of DCC-2036 on TNBC cells, the whole genome-wide transcriptome profile of MDA-MB-231 cells (a representative TNBC cell line) cultured with or without DCC-2036 was analyzed by cDNA microarray.

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Project description:The goal of this study is to compare mRNA expression profiles of the ACP52C-treated cells in time dependent manner. All cell lines were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. For the drug treatment, MDA-MB-231 and HepG2 cells were incubated in the presence of 2 μM ACP52C for 0, 12, 24, and 48 hours. 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). The library was prepared using the RNA seq3’ mRNA-Seq Library Prep Kit FWD. The constructed libraries were subjected to 150-bp two-end sequencing using an Illumina NextSeq 500 sequencer at Insilicogen. All procedures were performed following the manufacturer’s instructions. Tophat 2 and cufflinks were used for reads mapping and expected read counts, respectively. DEGs were analyzed using an edgeR program and functional annotation of genes were achieved using a DAVID program.

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Genome-wide maps in MDA-MB-231 cells treated with or without CPUL119(4.5 μM), CPUL129(1.8 μM), CPUL149(0.9 μM)

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