Comparing BMMSCs treated with PBS (Con group) or EM-eNMs (EM-eNMs group)
RNA sequencing. Total RNAs from aged BMMSCs (P10-12), with or without em-eNMs treatment, were extracted by Trizol reagent (Thermo Fisher Scientific, Cat. No. 15596026). Sequencing libraries were generated using the NEBNext(R) Ultra(TM) RNA Library Prep Kit for Illumina(R) (NEB, USA) following the manufacturer's recommendations. Samples were then sequenced on an Illumina HiSeq 3000 platform. Quality control of the RNA-seq data was performed using FastQC (v0.11.5) and the FASTX toolkit (0.0.13). The data were mapped to the human reference genome (NCBI build 37, Jul 2007, mm9) using HISAT2 (v.2.0.4). Three samples per group were used. Differentially expressed genes and transcripts were identified using Ballgown software (v.3.4.0). Genes were considered significantly differentially expressed if they showed a >=1.5-fold change and a P value < 0.05.