Genome-wide siRNA screen of genes regulating the Lipopolysaccharide-induced TNF-alpha response in human macrophages - GSE83824

The mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution to endotoxemia and sepsis. Here we describe a genome-wide siRNA screen to identify genes regulating the human macrophage TNF-? response to LPS. We include a secondary validation screen conducted with six independent siRNAs per gene to facilitate removal of off-target screen hits. We also provide microarray data from the same LPS-treated macrophage cells to facilitate downstream data analysis. These data provide a resource for analyzing gene function in the predominant pathway driving inflammatory cytokine expression in human macrophages.

THP-1 cells were stimulated with 0 and 10 ng/ml of LPS separately for 4hrs. Three replicates for each condition.

Lipopolysaccharide exposure (2021 ICD-10-CM code* = Not Applicable)

Signal data was extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log 2 scale. Probes that didn't show detection p-value < 0.1 in at least 2 arrays were removed from the dataset. After filtering probes, quantile normalization was applied across all arrays.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83824