RNA-Seq analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice

ABSTRACT: Purpose: The goals of this study are to compare CD115- monocytes to CD115+ monocytes from naïve and tumor-bearing mice (EL4) with high-throughput data analysis. Methods: CD115- monocytes and CD115+ monocytes were sorted by flow cytomentry separatly. Total RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) and residual DNA was removed with a DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. Samples were loaded onto a 1% agarose gel before electrophoresis. DNA-free conditions were confirmed by SYBR Gold staining (Invitrogen). The quantity and the quality of RNA was evaluated by Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) and bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). RNA-Seq libraries were prepared with 1 μg of total RNA from two biological replicates of each group using TruSeq Stranded mRNA LT Sample Prep Kit and analyzed by Illumina Sequencer (both from Illumina, San Diego, CA, USA). Results: We found 1,723 differetially expressed genes (DEGs) between CD115- monocytes and CD115+ monocytes (cutoff value was set at 2-fold). DEGs of interest are invoved in granulocyte, transcription factors, mononuclear phagocytes, and angiogenesis. Conclusions: Our study represents the first detailed DEGs analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice. Our results show that CD115- monocytes may have a closer relationship with neutrophils or PMN-MDSCs than the CD115+ monocytes. Also, our overall transcriptomic analysis further suggests that CD115- M-MDSCs and monocytes are separate subsets of monocytic cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE199008 | GEO | 2022/03/22

REPOSITORIES: GEO