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E-GEOD-15991 - shRNA profiling of human hepatocyte HepG2 cells knocked down for HNF4 to investigate its role in inflammatory response

Status
Submitted on 6 May 2009, released on 16 May 2009, last updated on 10 June 2011
Organism
Homo sapiens
Samples (16)
Array (1)
Protocols (5)
Description
To obtain a genomic view of hepatocyte nuclear factor-4α (HNF-4α) in the regulation of the inflammatory response, microarray analysis was used to probe the expression profile of an inflammatory response induced by cytokines in a model of knock-down HNF-4α HepG2 cells. The results indicate an extensive role for HNF-4α plays in the regulation of a large number of the liver-specific genes. Majority of genes (71%) affected by cytokine treatment are also affected by HNF-4α knock-down. This significant overlap suggests that HNF-4α may play a role in regulating the cytokine-induced inflammatory response. Experiment Overall Design: The different treated HepG2 cells were grouped into 4 groups (four replicates in each group): Group1, Control; Group2, HNF-4α shRNA treated cells; Group3, cytokine treated group; Group4, HNF-4α shRNA and cytokine treatments. RNA extraction and hybridization on Affymetrix microarrays were processed. The expression profiles between different groups were analyzed and compared. In order to explore the function of HNF-4α in the inflammatory response, a set of 170 genes annotated as inflammatory response was obtained from GO (geneotology.org), the enrichments of these inflammatory genes were analyzed in different treated groups.
Experiment types
RNAi profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-15991.idf.txt
Sample and data relationshipE-GEOD-15991.sdrf.txt
Raw data (1)E-GEOD-15991.raw.1.zip
Processed data (1)E-GEOD-15991.processed.1.zip
Array designA-AFFY-37.adf.txt
R ExpressionSetE-GEOD-15991.eSet.r
Links