January 28, 2026 Dataset Open Access

Bulk RNA-sequencing of murine bone marrow-derived macrophages upon treatment with live or apoptotic thymocyte-derived extracellular vesicles

Lorenz Adlung

Researcher(s)

To investigate the differential effects of extracellular vesicles (EVs) derived from live versus apoptotic cells on macrophage function, we performed bulk RNA sequencing on murine bone marrow-derived macrophages (BMDMs) treated with EVs isolated from live thymocytes (liveT-EVs) or apoptotic thymocytes (aT-EVs). BMDMs were generated from C57BL/6J mice and differentiated over seven days. On day 7, cells were treated for 24 hours with either liveT-EVs or aT-EVs. Apoptosis in donor thymocytes was induced by 24-hour culture following initial harvest, and EVs were isolated via differential ultracentrifugation. RNA was extracted using QIAshredder columns and the RNeasy mini Kit (Qiagen), with three biological replicates per condition.

Library preparation and transcriptome sequencing were performed by BGI using 100 bp paired-end reads on the DNBSEQ platform. Reads were aligned to the mouse reference genome GRCm39 using STAR aligner (version 2.7.10b). Differential gene expression analysis was performed using DESeq2 (version 1.40.2), and pathway analysis was conducted using clusterProfiler (version 4.8.3) and enrichR (version 3.4). This dataset reveals distinct transcriptomic signatures induced by EVs depending on the viability status of their donor cells, with apoptotic cell-derived EVs notably activating nitric oxide-related pathways in target macrophages.