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Series GSE53004 Query DataSets for GSE53004
Status Public on May 01, 2014
Title Toxicogenomics in the 3T3-L1 cell line, a new approach for screening of obesogenic compounds
Organism Mus musculus
Experiment type Expression profiling by array
Summary The obesogen hypothesis states that exposure to environmental compounds early in life or throughout lifetime might have an influence on obesity development. In this paper a new approach for obesogen screening is proposed, namely the use of transcriptomics in the 3T3-L1 pre-adipocyte cell line. Based on the data from a previous study of our group using a lipid accumulation based adipocyte differentiation assay, several humanly relevant obesogenic compounds were selected: reference obesogens [Rosiglitazone (ROSI), Tributyltin (TBT)], test obesogens [Butylbenzyl phthalate (BBP), butylparaben (BP), propylparaben (PP), Bisphenol A (BPA)] and non-obesogens [Ethylene Brassylate (EB), Bis (2-ethylhexyl)phthalate (DEHP)].
In this paper, the high stability and reproducibility of the 3T3-L1 gene transcription patterns over different experiments and cell batches was shown. Obesogens and non-obesogen gene transcription profiles were clearly distinguished using hierarchical clustering. Furthermore, a gradual distinction corresponding to differences in induction of lipid accumulation could be made between test and reference obesogens based on transcription patterns, indicating the potential use of this strategy for classification of obesogens. Marker genes that are able to distinguish between non, test and reference obesogens were identified. Well known genes involved in adipocyte differentiation, as well as genes with unknown functions were selected, implying a potential adipocyte related function of the latter. Cell physiological lipid accumulation was well predicted based on transcription levels of the marker genes, indicating the biological relevance of omics data.
In conclusion, this study shows the high relevance and reproducibility of this 3T3-L1 based in vitro toxicogenomics tool for classification of obesogens and biomarker discovery.
Overall design The hybridization design was a reference design (reference sample was a mixture of equal aliquots from control and exposed samples), recommended for class discovery purposes (Knapen et al. 2009). The reference sample was labeled with Cy5, and the exposed samples with Cy3. Three biological replicates were measured for every condition.
Contributor(s) Pereira-Fernandes A, Vanparys C, Hectors TL, Vergauwen L, Knapen D, Jorens P, Blust R
Citation(s) 24848799
Submission date Dec 04, 2013
Last update date Nov 01, 2017
Contact name Anna Pereira-Fernandes
Organization name University of Antwerp
Department Biology
Street address Groenenborgerlaan 171
City Antwerp
ZIP/Postal code 2020
Country Belgium
Platforms (1)
GPL11202 Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Probe Name version)
Samples (30)
GSM1280255 DMSO repl 1 vs Reference
GSM1280256 DMSO repl 2 vs Reference
GSM1280257 DMSO repl 3 vs Reference
BioProject PRJNA230649

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
GSE53004_RAW.tar 185.1 Mb (http)(custom) TAR (of GPR)
GSE53004_genes.BBPvsDMSO.txt.gz 297.1 Kb (ftp)(http) TXT
GSE53004_genes.BPAvsDMSO.txt.gz 305.6 Kb (ftp)(http) TXT
GSE53004_genes.BPvsDMSO.txt.gz 306.0 Kb (ftp)(http) TXT
GSE53004_genes.DEHPvsDMSO.txt.gz 278.8 Kb (ftp)(http) TXT
GSE53004_genes.EBvsDMSO.txt.gz 283.0 Kb (ftp)(http) TXT
GSE53004_genes.MDIvsDMSO.txt.gz 309.5 Kb (ftp)(http) TXT
GSE53004_genes.PPvsDMSO.txt.gz 303.6 Kb (ftp)(http) TXT
GSE53004_genes.ROSIvsDMSO.txt.gz 308.2 Kb (ftp)(http) TXT
GSE53004_genes.TBTvsDMSO.txt.gz 306.5 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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