Project description:We performed RNA-seq on dTAG-NUDT21 HCT116 cells treated with DMSO+JTE-607 or dTAGV1+JTE-607 for 48 hours with 4 biological replicates
Project description:The majority of transcription studies examine steady-state RNA . However steady-state RNA is not a true reflection of the transcriptome, because the RNA levels are affected by both transcription rate and degradation rate. In this experiment we measured the amount of transcription occurring in HCT116 colon cancer cells, regardless of degradation, using GRO-seq (global nuclear run-on sequencing). This information demonstrates that many genes have a pile-up of transcriptionally-engaged polymerase near their 5'-end. Nuclei were prepared from HCT116 cells (treated for 1hr with DMSO as control for additional GRO-seq experiments to be reported separately). Transcription run-on was performed (as per Core, L.J., Waterfall, J.J., and Lis, J.T. (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848) and nascent RNAs were purified and sequenced.
Project description:This study accompanies an adapted Cell Painting assay applied to 3D colorectal cancer spheroids (BioStudies S-BIAD2254). To relate image-based morphological profiles to transcriptional responses, bulk 3'-end RNA-seq was performed on HCT116 spheroids grown in ultra-low attachment 384-well plates and treated for 48 h with 5-fluorouracil (10 uM), olaparib (3 uM), or 0.1% DMSO vehicle. Gene-level differential expression and Hallmark pathway enrichment were used to characterise the drug-induced transcriptional programs underlying the observed morphological phenotypes.
