Project description:To compare the impact of several TP53 mutant variants in an isogenic setting, different TP53 mutations were introduced in HCT116 colorectal carcinoma cells. This parental cell line is wild-type for TP53 and shows a prototypical p53 response. To ensure unambigous genotype-phenotype correlations, the cell were haploidized prior to CRISPR-editing by introducing inactivating deletions of intronic splicing into one of the two TP53 alleles, leaving only one functional copy of TP53. The remaining TP53 allele was altered by inserting a LoxP-flanked transcriptional stop cassette (Lox-Stop-Lox, LSL) into intron 4, which allowed reversible silencing of TP53 expression. The LSL cassette was then specifically targeted with CRISPR/Cas9 to introduce a variety of different mutant p53 alleles. The competency of the mutated p53 allele to induce a p53 response upon activation using Nutlin-3a was then assessed in an RNAseq experiment.
Project description:The aim of this experiment was to assess the on- and off-target effects of MAPT-AS1 expression, and whether mutations/deletions to MAPT-AS1 alter these effects. SHSY5Y cells stably expressing variants of MAPT-AS1 were analyzed by Riboseq and Quantseq.
Project description:To identify if the alteration of Myosin activity identified in DPRs expressing cells induced alterations in the transcriptome profile of cells. For that purpose, we compared the changes in HEK293 cells transcriptome induced by a known myosin activity disruptor, Blebbistatin, with DPRs expressing cells .
Project description:RNA-seq of differentiated organoids (day 7) from a patient with an AGR2 mutation, patients with ulcerative colitis, or non-IBD controls. After 6 days differentiation, organoids were treated for 24 hours with Tunicamycin (T7765, Sigma Aldrich,1 µg/ml) or vehicle control (0.1 % DMSO).
Project description:Effect of LPA-Mixture (16:0, 18:0 18:1 18:2, 20:4) and LPAR2 specific (H2L5186303) or LPAR1 specific (Ro6842262) Inh. in OC91s cells.
Project description:Patient-derived intestinal organoids provide an excellent tool to unravel mechanisms underlying ulcerative colitis (UC). Fresh biopsies, to isolate crypts and culture organoids, were obtained from both inflamed and non-inflamed regions from eight patients with active UC (Mayo endoscopic subscore ≥2), and from eight non-IBD controls.To address the inflammatory character of ex vivo organoids, we compared the transcriptome of biopsies, crypts and organoids derived from inflamed, and non-inflamed regions and aimed to (re-)induce inflammation ex vivo.