Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations

Mahmoud Ahmed, Do Sik Min, Deok Ryong Kim

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


The 3T3-L1 cell line is used as an adipocyte differentiation model for the analysis of genes specifically expressed during the differentiation course. This cell model has several applications in obesity and insulin resistance research. We built a data resource to model gene expression of differentiating and mature adipocytes in response to several drugs and gene manipulations. We surveyed the literature survey for microarray datasets of differentiating 3T3-L1 cell line sampled at one or more time points under genetic or pharmacological perturbations. Data and metadata were obtained from the gene expression omnibus. The metadata were manually curated using unified language across the studies. Probe intensities were mapped and collapsed to genes using a reproducible pipeline. Samples were classified into none, genetically or pharmacologically modified. In addition to the clean datasets, two aggregated sets were further homogenized for illustration purposes. The curated datasets are available as an R/Bioconductor experimental data package curatedAdipoArray. The package documents the source code of the data collection, curation and processing. Finally, we used a subset of the data to effectively remove batch effects and reproduce biological observations. Database URL

Original languageEnglish
Pages (from-to)600-608
Number of pages9
Issue number1
Publication statusPublished - 2020 Jan 1

Bibliographical note

Funding Information:
This study was supported by the National Research Foundation of Korea (NRF) grant funded by the Ministry of Science and ICT (MSIT) of the Korea government [2015R1A5A2008833 and 2020R1A2C2011416]. We thank all the lab members for the critical discussion of the various drafts of this manuscript.

Publisher Copyright:
© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

All Science Journal Classification (ASJC) codes

  • Histology
  • Cell Biology


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