Gene counts matrix for RNA-seq of metal nanoparticles

A549 cells were seeded at a density of 1× 105 cells/well in 12-well plates (Thermo, USA). In general, the 10% inhibitory concentration (IC10) was used as the maximal concentration of each sample for the concentration-dependent transcriptome experiment. If a sample showed no cytotoxicity, the 0.1% stock solution was chosen as the maximum concentration.

Fivefold serial dilutions were prepared for each set of samples (file: Concentration group.csv). After 24 hours of exposure, total RNA was obtained using a RNeasy Mini Kit (Qiagen, Hilden, Germany), and the 72 RNA samples (for the 70 treatment groups and two solvent control groups) were stored at -80 °C before use. The RNA concentrations were measured via a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, MA) and a Quant-iT RNA HS Assay Kit. The RNA sample quality was measured with an Agilent 2100 Bioanalyzer (Agilent Technologies). Using an Ion AmpliSeq Library Kit 2.0 and Ion AmpliSeq custom panels, 10 ng of total RNA was taken per sample to construct a sequencing library for the human omics approach (Thermo Fisher Scientific, Waltham, MA). After the sequencing library was constructed, sequencing was performed via an Ion Torrent Proton (Life Technologies, USA). The Coverage Analysis plugin of the Ion Torrent Service was applied to count and classify 1200 human genes in the RHT panel.

Reduced human transcriptome (RHT) technology is based on molecular biology, in which a small number of genes in a gene network or pathway can represent the expression of most other genes in the network. The 1200 genes (file: Human 1200 Reduced Genome.csv) screened out can cover 90% of the KEGG pathways and 97% of the GO BP pathways and best preserve the full transcriptome map information.