Omicsoft software

To evaluate assay efficacy, Ct values were calculated using the BioMark Real-Time PCR Analysis software (Fluidigm). Ct values between 40 and 24 corresponded to detectable expression levels and values < 24 represented quantifiable expression levels. Ct values were normalized to those of endogenous controls by subtracting average CCCTC-binding factor (CTCF) and TATA-binding protein (TBP) expression levels, using OmicSoft™ software (Qiagen). The most stable reference genes for normalization were identified using a geNorm test on qbase⁺ software (qPCR analysis). A second normalization was performed using a common experimental control sample in the three experiments to correct potential technical qPCR bias. The OmicSoft™ Array viewer version 10.0.1.96 software was used for normalization, and -ΔCt was represented using boxplots according to the median, standard deviation of groups, and heatmaps.

On day 10 or 11 of DC or MΦ culture, the contents of cells were extracted via application of TRIzol (Thermo Fisher Scientific, Waltham, MA). To isolate RNA from samples, a chloroform solvent extraction was performed according to manufacturer instructions. Next, RNA was purified using a kit, RNA Clean & Concentrator with DNAse (Zymo Research, Irvine, CA). The DNA Technologies Core at UC Davis assessed RNA quality (score>7.0), performed Batch 3’Tag-Seq library preparation, and sequenced using an Illumina NextSeq sequencer (Illumina, San Diego, CA). For analysis, reads were trimmed, aligned, and quantified for gene counts using OmicSoft software (Qiagen, Hilden, Germany). Dimensional reduction for principal component analysis (PCA) plots was also performed in the OmicSoft software.