Transcriptome and translatome analysis of THP1 cells with doxycycline induced FXR1 Knockdown

FXR1 depletion in THP1 cells causes changes in polysome associated mRNAs. This leads to a distinct translatome in the cell. The experiment is comprised of 16 HuGene 2.0 ST arrays, profiling input RNA and sucrose-gradient-purified polysomal RNA obtained from leukemic cells transfected with pTRIPZ inducible non-silencing control or cells transfected with a TRIPZ lentiviral vector containing an shRNA targeting the gene FXR1, collected either during normal mitotic growth (S+ phase) or after inducing cell cycle arrest (G0 phase). Total RNAs and RNAs associated with polysomes were purified from THP1 cells (control shRNAs), THP1 cells (FXR1 knockdown) under proliferating and serum starvation conditions and hybridization on affymetrix microchips. Polysomes were isolated by fractionation on sucrose gradients. RNA was purified from either total cell lysate and or from only polysome fractions. Translatome change was analysed after normalizing mRNA levels on polysome to their level in total cell lysate.