Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes

Abstract

The 3T3-L1 pre-adipocyte cell line is widely used to study the fat cell differentiation in vitro. Researchers also use this cell model to study obesity and insulin resistance. We surveyed the literature, the gene expression omnibus and the sequence read archive for RNA-Seq and ChIP-Seq datasets of MDI-induced 3T3-L1 differentiating cells sampled at one or more time points. The metadata of the relevant datasets were manually curated using unified language across the original studies. The raw reads were collected and pre-processed using a reproducible state-of-the-art pipeline. The final datasets are presented as reads count in genes for the RNA-Seq and reads count in peaks for the ChIP-Seq dataset. The curated datasets are available as two Bioconductor experimental data packages curatedAdipoRNA and curatedAdipoChIP. In addition, the packages document the source code of the data collection and the pre-processing pipelines. Here, we provide a descriptive analysis of the datasets with context and technical validation.