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Series GSE20948 Query DataSets for GSE20948
Status Public on May 01, 2010
Title The Effect of Hepatitis C Virus Infection on Host Gene Expression
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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. The expression of host genes involved in cellular defence mechanisms (apoptosis, proliferation and anti-oxidant responses), cellular metabolism (lipid and protein metabolism) and intracellular transport (vesicle trafficking and cytoskeleton regulation) was significantly altered by HCV infection. The gene expression patterns identified provide insight into the potential mechanisms that contribute to HCV associated pathogenesis. These include an increase in pro-inflammatory and pro-apoptotic signalling and a decrease in the anti-oxidant response pathways of the infected cell.
 
Overall design 5x105 Huh7 cells were seeded in 25cm2 culture flasks and infected in triplicate either with the genotype 2a HCV clone, JFH-1 at a multiplicity of infection (MOI) of 3 or mock infected with an equal volume of concentrated conditioned growth medium. At 6, 12, 18, 24 and 48 hours post-infection, cellular RNA was extracted using TRIzol reagent (Invitrogen). Trizol lysates were shipped to Expression Analysis (NC, USA) where RNA was purified, quality tested using the Agilent Bioanalyser and hybridised onto Human U133 Plus 2.0 Affymetrix microarray chips for fluorescence data acquisition. In summary, a total of 30 RNA samples were analysed including 3x mock infected samples taken at 6, 12, 18, 24 and 48 hours post-treatment and 3x JFH-1 infected samples taken at 6, 12, 18, 24 and 48 hours post-infection. Two samples (Mock_6hrs_1 and JFH-1_6hrs_1) did not pass our data quality control measures and were therefore excluded from the statistical analysis.
 
Contributor(s) Blackham SL, Baillie A, Al-Hababi F, Remlinger K, You S, Hamatake R, McGarvey MJ
Citation(s) 20200238
Submission date Mar 18, 2010
Last update date Mar 25, 2019
Contact name Michael J McGarvey
E-mail(s) m.mcgarvey@imperial.ac.uk
Phone +44 (0)20 594 9035
Organization name Imperial College London
Department Medicine
Street address Norfolk Place
City London
ZIP/Postal code W2 1PG
Country United Kingdom
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (28)
GSM523800 Huh7 cells_JFH-1 Infected 6 hours_ rep2
GSM523801 Huh7 cells_JFH-1 Infected 6 hours_ rep3
GSM523802 Huh7 cells_JFH-1 Infected 12 hours_ rep1
Relations
BioProject PRJNA124431

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE20948_RAW.tar 135.4 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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