Project description:Transcriptional profiling of human hepatocarcinoma comparing Huh-7 and SNU-739. Two-condition experiment, normalized ratio represented by Huh-7/SNU-739. Biological replicates: 2 Huh-7 replicates, 2 SNU-739 replicates.
Project description:Human SNU cell lines derived from hepatocellular carcinomas associated with chronic hepatitis B virus (HBV) infection were examined. The analysis of intracellular RNA and DNA markers of HBV replication and examination of HBV RNA reads coverage of selected regions on HBV-related RNAs and polyadenylation positions within HBV sequence using RNA-sequencing suggested absence of HBV replication in SNU-423, SNU-368 SNU-398, SNU-182, SNU-449, SNU-475, SNU-354, SNU-739 and SNU-387 cells, while SNU-761 and SNU-886 still could maintain residual HBV replication. The undetectable intracellular HBV core antigen (HBcAg) and absence of significant levels of secreted core-associated and virion-associated HBV DNA confirmed the absence or profound suppression of HBV replication in parental SNU cell lines. Various 5'-human-HBV-3' and 5'-HBV-human-3' RNAs transcribed from integrated HBV DNA were found in most of SNU cell lines. The 5'-HBV-human-3' junctions suggested that several SNU cell lines could generate 5'-HBV-human-3' RNAs encoding HBV envelope proteins. The known and novel spliced HBV RNAs were detected in SNU-886, SNU-739, SNU-387, SNU-761, and SNU-354 cells. At least some of them were generated independently of HBV replication. All SNU cell lines could not support efficient HBV replication after transfection with the vector initiating efficient HBV replication in Huh7 cells. This was reflected by three distinct accumulation patterns of HBV replication markers, undetectable intracellular HBcAg, and by the lack of considerable levels of secreted core-bound and virion-associated HBV DNA. Overall, SNU cell lines represent valuable model systems for detailed analysis of integrant-transcribed HBV RNAs, spliced HBV RNAs, and mechanisms of suppression of HBV genome replication.
Project description:RNA transcriptome sequencing analysis was performed in SNU-668 Erastin-resistant cells and SNU-668 parental cells, SNU-484 RSL3-resistant cells and SNU-484 parental cells
Project description:a microarray analysis of long noncoding RNAs was performed in exosomes from SNU-668 Erastin-resistant cells and parental SNU-668 cells
Project description:The expression profiling of HBV-transfected Huh-7 cells and control cells. Hepatocellular carcinoma (HCC) is one of major malignant disease worldwide, and patients with chronic hepatitis B virus (HBV) infection have a high risk of developing HCC. Via microarray gene expression analysis, we detected the gene alteration in HBV transfected hepatoma cells.
Project description:Sorafenib is the global standard of care for patients with advanced hepatocellular carcinoma. It has marginal efficacy and patients invariably develop therapeutic resistance. The primary goal of this project was to comprehensively chratcerize the molecular profile of sorafenib resistant Huh-7/SR1 and Huh-7/SR2 cells compared to their parental counterpart Huh-7 cells, and discover potential new druggable targets which can overcome sorafenib resistance.
Project description:We report the application of chromatin immunoprecipitation sequencing (ChIPseq) and ATAC for high-throughput profiling of histone modifications in Huh 7 cells.
Project description:Genomes are pervasively transcribed leading to stable and unstable transcripts that define functional regions of genomes and contribute to cellular phenotypes. Defining comprehensive nascent transcriptomes is pivotal to understand gene regulation, disease processes, and the impact of extracellular signals on cells. However, currently employed methods are laborious, technically challenging and costly. We developed single-nucleotide resolution 4sU-sequencing (SNU-Seq), involving pulse labelling, biotinylation and direct isolation of nascent transcripts. Artificial poly-(A)-tailing of the 3’ most nucleotide of nascent transcripts ensures oligo-d(T) primer-based library preparation and sequencing using commercial 3’ RNA-Seq kits. We show that SNU-Seq is a cost-effective new method generating even read profiles across transcription units. We used SNU-Seq to identify transcription elongation parameters, to map usage of polyadenylation (PAS) sites and novel enhancers. Remarkably, 4sU labelled nascent RNA accumulates short ~100nt transcripts that map to the 5’ end of genes. We show that isolation of these short nascent RNA and sequencing the 5’ and 3’ ends using size-selected SNU-Seq (ssSNU-Seq) provides highly sensitive annotations of mapped and novel TSSs, promoter-proximal pause/termination sites. Thus, SNU-seq and ssSNU-seq combined yield comprehensive transcriptomics data at low cost with high spatial and temporal resolution.
Project description:Gene expression profiles of PBMCs in patients with hepatocarcinoma after ablative treatment. Results provide the information of changes in PBMPs transcriptome following ablative treatment of hepatocarcinoma.