ABSTRACT

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

https://bioconductor.org/packages/curatedAdipoArray

摘要

3T3-L1细胞系用作脂肪细胞分化模型，用于分析在分化过程中特异性表达的基因。该细胞模型在肥胖和胰岛素抵抗研究中有多种应用。我们建立了一个数据资源，以对几种药物和基因操作的反应，对分化和成熟的脂肪细胞的基因表达进行建模。我们调查了在基因或药理学扰动下在一个或多个时间点采样的分化3T3-L1细胞系分化的微阵列数据集的文献调查。从基因表达综合获得数据和元数据。在研究中使用统一语言手动整理元数据。使用可重现的管线将探针强度作图并折叠成基因。样品分类为无，经过基因或药理学修饰。除了干净的数据集，还对两个聚合集进行了均化以用于说明目的。整理的数据集可作为R / Bioconductor实验数据包curatedAdipoArray获得。该软件包记录了数据收集，管理和处理的源代码。最后，我们使用了数据的子集来有效消除批处理效应并重现生物学观察结果。

数据库URL

https://bioconductor.org/packages/curatedAdipoArray