Expression data from human amniotic fluid-derived stem cells (AFSC) treated with ethanol
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE13569 | GEO | 2009/09/30
SECONDARY ACCESSION(S): PRJNA110673
REPOSITORIES: GEO
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Project description:The effects of ethanol may vary from induction of apoptosis to the inhibition of proliferation, differentiation, migration or other function. The complex and diverse response of fetal cells to ethanol has prompted us to use a bioinformatics approach to study the effect of ethanol on fetal stem cells derived from the amniotic fluid-derived (AFSC). To characterize the global response of human AFSC to ethanol, gene expression profiles of AFSC treated with or without 100mM ethanol for 48 hours were analyzed. Experiment Overall Design: Two microarrays were performed (AFSC sealed with parafilm for 48 hours treated with or without 100 mM of ethanol). Total RNA was isolated using RNA Bee according to manufacturer's instructions. Fragmented antisense cRNA was used for hybridizing with human U133 A arrays (Affymetrix, Inc. Santa Clara, CA, USA) at the Core Genomic Facility of Wake Forest University School of Medicine. Raw CEL files were provided by the Microarray Core Facility of the Wake Forest University School of Medicine and were then analyzed with a software package AffylmGUI (Affymetrix LIMMA, Linear Models for Microarray Data, Graphical User Interfaces). AffylmGUI reads the raw Affymetrix CEL files directly, summarizes the gene expression values using RMA, and then uses LIMMA to identify statistically significant differences in gene expression. LIMMA fits a linear model for every gene (like ANOVA or multiple regression analysis), and adjusts P values for multiple testings. Differentially expressed genes were identified with a fold change > 1.8.
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Project description:Amniotic fluid stem cells (AFSCs) are of interest in regenerative medicine as a non-controversial and potentially 'abundant' source of stem cells. Progress has been made in understanding amniotic fluid stem cell biology, and amniotic fluid-derived cells have been induced to form neurons, osteoblasts, muscle cells, and others. Our study evaluates change in the genome-wide expression profile of amniotic fluid stem cells during in-vitro culture, using Affymetrix U133 Plus 2.0 microarray chips. We found that only 3.08% of gene probes were differentially expressed from early to late passage of AFSC culture. The differentially expressed genes were related to biological processes or cellular function - including transcription factors, protein kinases, and cytokines/growth factors. Other gene-sets of interest were oncogenes and tumor suppressor genes, which were a very small number of genes. We further analyzed the gene sets of interest using NIH DAVID and GSEA bioinformatics databases for gene annotations analysis. Applying false discovery rate correction, there was no significant difference in the genome-wide expression profiling between early and late passage. AFSCs maintain their genome-wide expression profile during in-vitro culture. Amniotic fluid-derived c-kit-positive cells were maintained in stem cell culture and genome-wide expression changes were studied and compared between early passage and late passage in culture.
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