Stimulus-Response signaling dynamics characterize macrophage polarization states

RNAseq data from hMPDMs (HoxB4 myeloid progenitor derived macrophages), BMDMs (bone-marrow derived macrophages), and Raw264.7 cell line in unstimulated condition and 3 hours post LPS stimulation (lipopolysaccharide). Gene expression demonstrates similarities between hMPDMs and BMDMs supporting use of hMPDMs in this study of NFkB stimulus response signaling dynamics, whereas Raw264.7 cells are more distinct from BMDMs in terms of expression LPS-inducible genes. Bone-Marrow Derived Macrophages (BMDMs) were cultured with standard methods, L929-conditioned medium. Raw 264.7 cells were cultured in DMEM 10 % FBS media. After LPS stimulation, cells were harvested at 3 hours. For PolyA+ RNA, cells were harvested in TRIzol reagent (Life Technologies, Carlsbad, CA). Then, DNA-free RNA was extracted from cell using DIRECTzol kit (Zymo Research, Irvine, CA) according to manufacturer’s instructions. After RNA extraction, libraries for polyA+ RNA were prepared using KAPA Stranded RNA-Seq Kit for Illumina Platforms (KAPA Biosystems, Wilmington, MA) according to the manufacturer’s instructions. Resulting cDNA libraries were single-end sequenced with a length of 50bp on an Illumina HiSeq 2000 (Illumina, San Diego, CA).