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Series GSE20659 Query DataSets for GSE20659
Status Public on Jun 01, 2010
Title A Comparative Study of Genome Wide Transcriptional Profiles of Primary Hepatocyte in In Vitro Cultures
Organism Rattus norvegicus
Experiment type Expression profiling by array
Summary The liver is one of most important organs in our bodies. It performs many essential functions including metabolism, synthesis, secretion, detoxification, and storage. Hepatocytes are the principal cell type in the liver and are involved in multiple liver-specific functions. There have been several efforts to develop in vitro culture systems capable of maintaining hepatocyte-specific phenotype over long time periods. In hepatic tissue engineering, two commonly used culture systems are the collagen sandwich and monolayers of cells.  In this study, genome-wide gene expression profiles of primary hepatocytes were measured over an 8-day period for each cell culture system using Affymetrix GeneChips and analyzed via Gene Set Enrichment Analysis (GSEA), which is a powerful method to elicit biologically meaningful information from microarray data at the level of gene sets. Results indicate that the gene expression in hepatocytes in collagen sandwich cultures gradually diverges from that in monolayer cultures. Gene sets up-regulated in collagen sandwich cultures include those associated with liver metabolic and synthetic functions.  These functions are associated with lipid, amino acid, carbohydrate, and alcohol metabolism and bile acid synthesis. Nuclear receptors are up-regulated in collagen sandwiches 24 hours after seeding. Signals transmitted from these receptors may cause the up-regulation of other processes in subsequent days. Cytochrome-P450 monooxygenase expression was initially down-regulated but exhibited up-regulation after 72 hours. Our results provide a baseline for further explorations into the systems biology of engineered liver mimics as well as 2D and 3D co-cultures of primary hepatocytes and non-parenchymal cells.
 
Overall design To better understand differences in quality of in vitro growth of rat hepatocytes between culture on a monolayer of collagen gel and sandwiched between two layers of gel, we measured gene expression in hepatocytes in these two culture conditions in triplicate for four time points: 1 day, 2 days, 3 days, and 8 days of culturing. Overall, we obtained Affymetrix microarray data for 24 samples, divided to 12 samples from monolayer and double layer cultures each, each of which are divided into four time points with 3 sample replicates.
 
Contributor(s) Kim Y, Lasher CD, Milford LM, Murali TM, Rajagopalan P
Citation(s) 20412007, 21245926, 23895181
Submission date Mar 05, 2010
Last update date Oct 24, 2019
Contact name Chris Lasher
E-mail(s) lasher@vt.edu
Organization name Virginia Polytechnic and State University
Department Genetics, Bioinformatics, and Computational Biology
Lab Murali
Street address 103 Lucas Dr Apt B
City Blacksburg
State/province VA
ZIP/Postal code 24060
Country USA
 
Platforms (1)
GPL1355 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array
Samples (24)
GSM518405 Liver_single_gel_day1_rep1
GSM518406 Liver_single_gel_day1_rep2
GSM518407 Liver_single_gel_day1_rep3
Relations
BioProject PRJNA124881

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE20659_RAW.tar 60.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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