Transcriptome analysis on TDP43 and SRSF3 downstream genes and binding RNAs in MDA-MB231 cells by Next Generation Sequencing

TDP43 and SRSF3 has been reported to be RNA-binding proteins; however their roles in breast cancer progression has not been examined previously. Here, we performed RNA-seq on MDA-MB231 cells stably expressed sh-control, shTDP43, shSRSF3 or sh-TDP43 and sh-SRSF3 using lentivirus in duplicates. In addition, MDA-MB231 cells with stable expression of flag-TDP43 or flag-SRSF3 were also generated by using lentivirus. RIP-seq was also applied to identify binding RNA against Flag antibodies. Overall design: Kncoking down TDP43 or SRSF3 in these cells was achieved using stable expression of shRNA specific for TDP43 or SRSF3 gene using lentivirus. Stable infected cells were selected and harvested for RNA isolation in duplicates. RNA-seq was performed to study the effect of TDP43 or TDP43-knowdown in MDA-MB231. Examination of RNA immunoprecipitation in Flag-TDP43 and Flag-SRSF3 wtih Flag antibodies.