Project description:A biallelic mutation in the SPRTN gene is currently the only known single-gene mutation implicated in early-onset HCC, contributing to the development of liver cancer. The precise mechanism by which SPRTN mutations lead to HCC is not fully understood. The SPRTN protein is involved in repair of DNA damage caused by DNA-protein crosslinks (DPC). Spartan was silenced in HepG2 cells with siRNA that targets mRNA of Spartan using Lipofectamine RNAiMAX (Thermo Fisher).Total RNA was extracted with QIAzol (Qiagen) according to the manufacturer's protocol and transcribed into cDNA with High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems) according to the manufacturer's protocol to test level of silencing with RT-qPCR . The quality of RNA was tested with agarose electrophoresis and concentration was determined using Nanodrop. Samples were send to company providing RNA sequencing. Company did RNA quality check, sequencing and analysis of the results.
Project description:To determine the effects of UBL5 on genome-wide gene expression, we used UBL5 siRNA to knock down UBL5 in HepG2 and Huh7 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq.
Project description:To investigate the effect of IGFRIL/PTBP1 in HCC, we established HepG2 cell lines in which IGFRIL/PTBP1 mRNA has been degraded using siRNA.
Project description:The nucleolar scaffold protein NPM1 acts as a multifunctional regulator of cellular homeostasis, genome integrity, and stress response. We and others show that NPM1 is also involved in regulation of the autophagic pathway. As NPM1 binds to members of the GABARAP protein family, important for autophagy, we anticipate that this interaction is important for the role of NPM1 in autophagy. In order to identify NPM1-dependent GABARAPL1 interactors we performed HA-GABARAPL1 immunoprecipitation with siRNA-mediated NPM1 depletion.
Project description:ELK1 is a well-known target of the ERK branch (EGF-responsive) of the MAP kinase pathway. This transcription profiling experiment studied the effects of ELK1 depletion by siRNA and subsequent EGF stimulation.