Multi-omics data for pro-inflammatory and anti-inflammatory exposure to THP-1 macrophages

This data characterizes gene expression levels in THP-1 macrophages. The data was generated using RNA sequencing and analyzed with DeSeq2 (version 1.24.0). The analysis included raw count data and normalized count matrices obtained from DESeq2's dds_deseq objects. This data describes the methylation levels of individual CpG sites in THP-1 macrophages. The data was obtained using the Infinium MethylationEPIC v2.0 Kit (Illumina) and analyzed with the minfi package (version 1.46). Specifically, the data underwent quantile normalization using the preprocessQuantile function within minfi. Only CpG sites with a detection p-value less than 0.05 were included to obtain MatrixProcessedGEO.txt file. The beta values (bValues.xlsx) were obtained using the function “getBeta” from the same package, considering each time point individually. The macrophages were exposed to phorbol 12-myristate 13-acetate (PMA) for 48 hours, followed by treatment with either a combination of LPS (10 pg/ml) and interferon-gamma (IFNγ) (20 ng/ml) or a combination of interleukins 13 (IL-13) (20 ng/ml) and 4 (IL-4) (20 ng/ml) for 24, 48, and 72 hours.