Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine , Jinju, Republic of Korea.
College of Pharmacy, Yonsei University , Incheon, Republic of Korea.
Adipocyte. 2020 Dec;9(1):600-608. doi: 10.1080/21623945.2020.1829852.
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. https://bioconductor.org/packages/curatedAdipoArray.
3T3-L1 细胞系被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。这种细胞模型在肥胖和胰岛素抵抗研究中有多种应用。我们构建了一个数据资源，用于模拟分化和成熟脂肪细胞对几种药物和基因操作的基因表达。我们调查了文献中的微阵列数据集，这些数据集是在遗传或药理学干扰下，在一个或多个时间点对 3T3-L1 细胞系进行采样的。数据和元数据从基因表达综合数据库中获得。使用统一的语言对元数据进行了手动整理。使用可重复的管道将探针强度映射并合并到基因中。将样品分为未处理、遗传修饰或药物处理。除了干净的数据集外，还进一步均匀化了两个聚合数据集，以便说明问题。经过整理的数据集作为 R/Bioconductor 实验数据包 curatedAdipoArray 提供。该软件包记录了数据收集、整理和处理的源代码。最后，我们使用数据的一个子集有效地去除批次效应并重现生物学观察结果。 https://bioconductor.org/packages/curatedAdipoArray。
