GEO DataSets

Analysis of Huh7 hepatoma cells infected with JFH-1 Hepatitis C Virus (HCV) at 6, 12, 18, 24, and 48 hours post-infection. HCV is a leading cause of chronic liver disease. Results provide insight into molecular mechanisms that contribute to HCV-associated liver pathogenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 infection, 5 time sets

Platform:

GPL570

Series:

GSE20948

28 Samples

Download data: CEL

(Submitter supplied) Hepatitis C Virus is a leading cause of chronic liver disease. The identification and characterisation of key host cellular factors that play a role in the HCV replication cycle is important for the understanding of disease pathogenesis and the identification of novel anti-viral therapeutic targets. Gene expression profiling of HCV infected Huh7 cells by microarray analysis was performed to identify host cellular genes that are transcriptionally regulated by infection. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4160

Platform:

GPL570

28 Samples

Download data: CEL

(Submitter supplied) Host cells harbor various intrinsic mechanisms to restrict viral infections as a first line of antiviral defense. Viruses have evolved various countermeasures against these antiviral mechanisms. Here we show that N-Myc Downstream-Reguated Gene 1 (NDRG1) limits productive HCV infection by inhibiting viral assembly. Interestingly, HCV infection down-regulates NDRG1 protein and mRNA expression. Loss of NDRG1 increases the size and number of lipid droplets, which are the sites of HCV assembly. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) Hepatitis C Virus (HCV) has a extremely narrow host cell tropism and robustly infects only very few cell lines, most importantly the human hepatoma cell line Huh7. This cell line was isolated from a 57-year old Japanese male with fulminant hepatitis. Different subclones and passages of the Huh7 cell line show up to 1000-fold differences in HCV replication efficiency (permissiveness). In this experiment, we sought to identify factors responsible for these differences by correlating gene expression from eight different uninfected Huh7 variants with their respective HCV permissiveness. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL6480 GPL13264

39 Samples

Download data: TXT

(Submitter supplied) This study is complementary to the "Genome-wide analysis of host mRNA translation during hepatitis C virus infection" study (GSE44210), for which sucrose gradient ultracentrifugation followed by microarray analysis was used to identify translationally-regulated mRNAs (mRNAs associated with ribosomes) from JFH1-infected and uninfected Huh-7.5.1 cells. MicroRNA arrays have been conducted in parallel on total RNA from infected and uninfected cells, in order to determine if microRNA regulation could explain some of the mRNA translation regulations.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL13264

7 Samples

Download data: TXT

(Submitter supplied) Sucrose gradient ultracentrifugation followed by microarray analysis was used to identify translationally-regulated mRNAs (mRNAs associated with ribosomes) from JFH1-infected and uninfected Huh-7.5.1 cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

32 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL14546 GPL570

8 Samples

Download data: CEL, CHP, GFF, PAIR

(Submitter supplied) A powerful approach to study innate antiviral response is to compare the difference between wild type Huh7 cells, which do not support robust replication of hepatitis C virus (HCV)2, versus certain subclones of Huh7 cells that are permissive for HCV replication. We generated two permissive cell lines and two independent non-permissive subclone from Huh7 cells. We compared the global methylation pattern of these different cells and find that Huh7 cells exist as a heterogeneous population of cells with distinct patterns of gene methylation.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL14546

6 Samples

Download data: GFF, PAIR

(Submitter supplied) MX1 is a well-characterized interferon-induced antiviral gene. MX1 is activated by viral infection due to interferon production in cells. We treated non-permissive Huh7 cells and permissive HRP4 cells with interferon. We compared the expression of genes induced by interferon to determine host factors affecting HCV replication.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Membrane-bound transcription factor CREB3L1 undergoes Regulated Intramembrane Proteolysis (RIP) in response to Hepatitis C infection. RIP activates CREB3L1 so that it can prevent the growth of HCV infected cells through the action of downstream genes. We over-expressed a truncated form of CREB3L1 that does not require RIP to enter the nucleus. Cells over-expressing this truncated form were isolated by Fluorescence Activated Cell Sorting (FACS). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2 Samples

Download data: CEL, CHP

(Submitter supplied) Drugs directly targeting Hepatitis C (HCV) are often rendered useless by the high mutation rate of the virus. Thus, we deduce that targeting of host factor that affect HCV replication may provide enhanced therapy fort HCV infection. Hepatocyte cell line Huh7 is known to be non-permissive for Hepatits C (HCV) replication. Through a method developed by the Rice laboratory (Blight, K.J., et al., J Virol, 2002), selection of a small subset of permissive hepatocytes is possible. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4392

Platform:

GPL570

4 Samples

Download data: CEL, CHP

Analysis of hepatocyte cell line Huh7, non-permissive to hepatitis C virus (HCV) replication, and permissive cell lines Huh7.5 and HRP1. Results provide insight into host factors lost in cells permissive for HCV replication.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 cell line, 2 genotype/variation sets

Platform:

GPL570

Series:

GSE25156

4 Samples

Download data: CEL, CHP

(Submitter supplied) We developed transcriptome expression assisted non-directed proteome profiling (TEAnDPP) method to investigate host-pathogen interaction. Analysis of HCV replicon induced host-cell metabolism perturbation at gene expression level. Gene enrichment analysis on DEG revealed disulfide formation related genes were significantly enriched. Based on this observation, we addminitrated thiol reactive chemical probes to visualize reactive thiol profile in live cell, and observed unique reactivity profile. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

4 Samples

Download data: TXT

(Submitter supplied) Viruses lack the basic machinery needed to replicate and therefore must hijack host metabolism to propagate. Virus-induced metabolic alterations have yet to be systematically studied in the context of the host transcriptional regulation, offering insight into host-pathogen metabolic interplay. In this work we identified Hepatitis C Virus (HCV)-responsive regulators by coupling system-wide metabolic flux analysis with targeted perturbation of nuclear receptors in primary human hepatocytes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL571 GPL6244

9 Samples

Download data: CEL

(Submitter supplied) The chimpanzee is the only model other than man for investigating the pathogenesis of viral hepatitis types A through E. Studies of the host response, including microarray analyses, have relied on the close relationship between these two primate species: chimpanzee samples are commonly tested with human-based reagents. In this study, the host response to two dissimilar viruses, hepatitis E virus (HEV) and hepatitis C virus (HCV), was compared in multiple experimentally-infected chimpanzees. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

44 Samples

Download data: CEL, TXT

(Submitter supplied) Hepatitis C virus (HCV) infection is a global health problem. A number of studies have implicated a direct role of cellular lipid metabolism in the HCV life cycle and inhibitors of the mevalonate pathway have been demonstrated to result in an antiviral state within the host cell. Transcriptome profiling was also conducted on Huh-7 human hepatoma cells bearing subgenomic HCV replicons with and without treatment with 25-hydroxycholesterol (25-HC), an inhibitor of the mevalonate pathway that alters lipid metabolism, to assess metabolic determinants of pro- and antiviral states within the host cell. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

10 Samples

Download data: CEL

(Submitter supplied) Expression of human genes was compared in liver fibrosis stage F1, F2, F3, and F4 to find markers that can differentiate among each fibrosis stages and cirrhosis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14795

36 Samples

Download data: TXT

(Submitter supplied) Norwalk virus (NV) is a prototype strain of the noroviruses (family Caliciviridae) which have emerged as major causes of acute gastroenteritis worldwide. We have developed NV replicon systems using reporter proteins such as a neomycin resistant protein (NV replicon-bearing cells) and a green fluorescent protein (pNV-GFP), and demonstrated that these systems were excellent tools to study virus replication in cell culture. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL, CHP

(Submitter supplied) HCV+ cells were detected by smiFISH on liver section of a patient with hepatocellular carcinoma. Clusters of HCV+ and HCV- cells were captured by laser microdissection and transriptomes analysed by RNA sequening. Highly sensitive single molecule fluorescent in situ hybridization applied to frozen tissue sections of a hepatitis C patient allowed the delineation of clusters of infected hepatocytes. Laser micro-dissection followed by RNAseq analysis of HCV-positive and -negative regions from the tumoral and non-tumoral tissues from the same patient revealed HCV-related deregulation of expression of genes in the tumor and in the non-tumoral tissue.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: TXT