GEO DataSets

(Submitter supplied) We demonstrate that HBV infection induces expression of the proto-oncogenic miR17~92 and miR106b~25 clusters which target the downregulation of DDX5. Increased expression of these miRNAs is also detected in HBV-driven HCCs exhibiting reduced DDX5 mRNA. Stable DDX5 knockdown (DDX5KD) in HBV replicating hepatocytes increased viral replication, and resulted in hepatosphere formation, drug resistance, Wnt activation, and pluripotency gene expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

19 Samples

Download data: BED, BW, TXT

(Submitter supplied) Earlier studies linked sorafenib effectiveness to induction of ferroptosis. Herein we demonstrate sorafenib and mTKIs downregulate DDX5 in vitro and in vivo. To understand the effect of DDX5 downregulation, we compared TCGA-derived HCCs expressing low vs. high DDX5 focusing on ferroptosis-related genes. Glutathione Peroxidase 4 (GPX4), a key ferroptosis regulator, was significantly overexpressed in DDX5LOW HCCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) miRNA played an important role in the process of carcinogenesis in HBV related hepatocellular carcinoma. Therefore, we performed miRNA microarray to evaluate the miRNAs that expressed differentially between HCC tumor versus non-tumor liver tissues.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL10850

10 Samples

Download data: TXT

(Submitter supplied) We detected whole genome microarray expression profiling in three pairs of Dicer knockout coloretal cell lines and their normal controls, including DLD-1, RKO and HCT116.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL18402

6 Samples

Download data: TXT

(Submitter supplied) Hepatitis B virus (HBV) infection is a major health problem worldwide and chronically infected individuals are at high risk of developing cirrhosis and hepatocellular carcinoma (HCC). The molecular mechanisms whereby HBV causes HCC are largely unknown. By using a biologically relevant system of HBV infection of primary human hepatocytes (PHHs), we studied how HBV perturbs gene expressions and signaling pathways of infected hepatocytes, and whether these effects are relevant to productive HBV infection and HBV-associated HCC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) Mouse liver tumors (T) and non tumoral adjacent livers (NT) sorted from mice knock out for Axin1 gene specifically in the hepatocytes . 3 mice of the brother hood non deleted for Axin1 were used as controls (WT) We used microarrays to determine the differential expression between tumoral and non tumoral tissue.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL18802

16 Samples

Download data: CEL

(Submitter supplied) The molecular mechanisms whereby hepatitis B virus (HBV) induces hepatocellular carcinoma (HCC) remain elusive. We used genomic and molecular techniques to investigate host-virus interactions by mapping the entire liver of patients with HCC. We compared the gene signature of whole liver tissue (WLT) versus laser capture-microdissected (LCM) hepatocytes with intrahepatic expression of HBV. Gene expression profiling was performed on up to 17 WLT specimens obtained at various distances from the tumor center in individual livers of 11 patients with HCC and on selected LCM samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

140 Samples

Download data: CEL

(Submitter supplied) We screened a number of interferon inducible genes that may be involved in impeding HBV replication and found an anti-HBV activity in ISG20. ISG20 is an IFN-inducible 3’- to 5’-exonuclease, that degrades DNA and RNA and reduces antigen production in hepatocyte-derived cells A range of candidate genes whose expression was dependent on type I IFN stimulation were identified by gene arrays

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL

(Submitter supplied) Chronic HBV infection is a major cause of hepatocellular carcinoma (HCC) worldwide. The phenotypes of HCC are diverse, in part, due to mutations in distinct oncogenes and/or tumor suppressor genes. These genetic drivers of HCC development have generally been considered as major mediators of tumor heterogeneity. Using the liver-specific Pten-null HBV transgenic mouse model of chronic viral infection, a critical role for liver lobule zone-specific gene expression patterns in determining HCC phenotype is demonstrated. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL13112 GPL16417

20 Samples

Download data: FA, TXT

(Submitter supplied) Human primary hepatocytes isolated from chimeric mice were infected with HBV for 7 days. The comprehensive changes of miRNA levels were determined by miRNA array.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL17061

2 Samples

Download data: TXT

(Submitter supplied) Human primary hepatocytes isolated from chimeric mice were infected with HBV for 7 days. The comprehensive changes of mRNA levels were determined by mRNA array. Also, microRNA93 was delivered into those cells using bionanocapsules to determine the effects of rescue expression of miR93 in HBV replicating cells, because we found that miR93 expression level was downregulated in HBV-infected hepatocytes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13915

4 Samples

Download data: TXT

(Submitter supplied) Hepatitis B virus (HBV) infection is one of the major causes of hepatocellular carcinoma (HCC). Nucleos(t)ide analogue (NA) therapy is effective to reduce the HCC incidence, while it doesn’t completely prevent HCC. In this study, we explored the involvement of microRNA (miRNA) in the post-NA treatment HCC development. Chronic hepatitis B (CHB) patients who received NA treatment (n = 18) were divided into 2 groups: those who didn’t develop HCC during the follow-up period (non-HCC group) and those who developed HCC after treatment (HCC group). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL15018

42 Samples

Download data: TXT

(Submitter supplied) To clarify the role of miR-199a-3p in HCC, we carried out a gene expression microarray analysis using HCC cell lines (HLE and HLF) transfected with a miR-199a-3p mimic or a negative control. We found that 819 genes were downregulated (>2-fold) by miR-199a-3p in both cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16699

4 Samples

Download data: TXT

(Submitter supplied) Mrhl is a non coding RNA identified from mouse chromosome 8. It is a 2.4kb poly adenylated, nuclear restricted RNA expressed in multiple tissues. The 2.4 kb RNA also undergoes a nuclear processing event mediated through Drosha that generates an 80nt intermediate RNA. This study was aimed at understanding the functiion of mrhl by silencing the mrhl RNA in the mouse spermatogonial cells using a pool of siRNAs targeted against the mrhl and analyse the global gene expression change using Affymetrix mouse expression array. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Purpose:To understand the change in cellular metabolism and function for the overxepression of GSTZ1 or PCK1 in hepatoma cells. Methods:Total RNAs of AdGFP- , AdGSTZ1-, or AdPCK1-infected Huh7 cells were extracted using TRIzol (Invitrogen), following the manufacturer’s instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Novel Bio Ltd. Briefly, strand-specific RNA-seq libraries were prepared using the Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on Ion Torrent Proton sequencing platform. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

9 Samples

Download data: TXT

(Submitter supplied) HBV transcription and replication increases progressively throughout postnatal liver development with maximal viral biosynthesis occurring at around four weeks of age in the HBV transgenic mouse model of chronic infection. Increasing viral biosynthesis is associated with a corresponding progressive loss of DNA methylation. The loss of DNA methylation is associated with increasing levels of 5-hydroxymethylcytosine (5hmC) residues which correlates with increased liver-enriched pioneer transcription factor Forkhead box protein A (FoxA) RNA levels, a rapid decline in postnatal liver DNA methyltransferase (Dnmt) transcripts and a very modest reduction in Ten-eleven translocation (Tet) methylcytosine dioxygenase expression. more...

Organism:

Mus musculus; Hepatitis B virus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL29102

120 Samples

Download data: FA, TXT

(Submitter supplied) aCGH analysis of murine transgenic liver tissues affected with HCC, hybridized with age (18 months) and sex matched C57BL/6 mice. Moreover, 18months old C57BL/6 livers were hybridized with independent 18 months old C57BL/6 livers for control. Keywords: Array comparative genomic hybridization analysis (aCGH).

Organism:

Mus musculus

Type:

Genome variation profiling by array

Platform:

GPL8086

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18694 GPL20084

35 Samples

Download data

(Submitter supplied) Purpose: Chronic infection with hepatitis B virus is the leading global risk factor for the development of liver cancer. A large body of research has shown the many effects an HBV infection has on cellular physiology, particularly on pathways that may be involved in the development of HBV-associated diseases. Unfortunately, a significant portion of this research has been done in systems that may not mimic what is seen in a primary hepatocyte, and is not done on a transcriptome-wide scale. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20084

23 Samples

Download data: TXT

(Submitter supplied) Purpose: Chronic infection with hepatitis B virus is the leading global risk factor for the development of liver cancer. A large body of research has shown the many effects an HBV infection has on cellular physiology, particularly on pathways that may be involved in the development of HBV-associated diseases. Unfortunately, a significant portion of this research has been done in systems that may not mimic what is seen in a primary hepatocyte, and is not done on a transcriptome-wide scale. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

12 Samples

Download data: TXT