*3.2. RNA-Seq and de Novo Transcriptome Assembly*

To investigate the transcriptome modulation that occurred during exposure to iron nanoparticles, the KG1a and HL60 cells were treated with 50 μg/mL of FeNPs and PBNPs for 72 h, respectively. To obtain reliable global gene expression profiles, RNA-Seq was performed with as many as 12 samples, which consisted of two biological replicates of each treatment. Following the removal of adapters and low-quality reads, total mapped reads, unique mapped reads, and multiple reads were summarized and are presented in Table S2. The statistics of distribution of clean reads in different regions of the genome are shown in Figure S1. After alignment with the reference genome, the statistical results of mRNA peak insert size distribution were shown in Table S3. The correlation analysis of expression levels

among samples and the density map of gene expression level of all samples were further calculated to demonstrate reliability of the experiment and rationality of the sample selection (Figures S2 and S3).
