Additional file 1 of Decrease in membrane fluidity and traction force induced by silica-coated magnetic nanoparticles
Creators: name: Shin, Tae Hwan
name: Abdurazak Aman Ketebo
name: Lee, Da Yeon
name: Seungah Lee
name: Kang, Seong Ho
name: Shaherin Basith
name: Manavalan, Balachandran
name: Kwon, Do Hyeon
name: Sungsu Park
name: Lee, Gwang
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 1: Table S1. Ingenuity Pathway Analysis-based profiles of transcriptomic network-related genes in MNPs@SiO2(RITC)-treated cells. Table S2. RT-PCR and real-time PCR primer sequences for genes encoding transcriptomic network-related genes. Figure S1. Determination of size and homogeneity for MNPs@SiO2(RITC) and silica NPs using transmission electron microscope (TEM) analysis. TEM images of MNPs@SiO2(RITC) (a) and silica NPs (b). Scale bar = 50 nm. Figure S2. Evaluation of cytotoxicity in silica NPs and MNPs@SiO2(RITC) treated HEK293 cells. HEK293 cells were treated with silica NPs and MNPs@SiO2(RITC) for 12 h. The changes in cell viability were evaluated with MTS. Data represent mean ± SD of three independent experiments. N.S: Not significant. Figure S3. Low magnification laurdan GP images. Merged DIC and TIRFM images (upper panel) of HEK293 cells. Distributions of MNPs@SiO2(RITC) are shown in each lower panel. GP distributions ranged from −1.0 to 1.0. Scale bar= 2.5 µm. Figure S4. ROS generation in silica NPs and MNPs@SiO2(RITC)-treated cells. Evaluation of intracellular ROS generation using DCFH-DA after 12 h silica NPs and MNPs@SiO2(RITC) treatment in HEK293 cells. The intensity of non-oxidised DCFH-DA was used as a blank. Data represent mean ± SD of three independent experiments. *p &lt; 0.05 vs non-treated control, #p &lt; 0.05 compared between 0.1 and 1.0 µg/µl of NPs-treated cells. N.S: Not significant. Figure S5. Transcriptomic analysis of microarray in HEK293 cells treated with MNPs@SiO2(RITC) for 12 h. Network of lipid peroxidation and focal adhesion related genes was constructed algorithmically by IPA. (a) Transcriptome network of 0.1 µg/µl MNPs@SiO2(RITC)-treated cells and (b) prediction analysis for the network. Red and green areas indicate up- and downregulated genes, respectively. Orange and blue colours indicate activation and suppression. The lines indicate indirect (dotted) or direct (solid) relationship. Differentially expressed genes obtained from microarray data (genes with &gt; 3-fold change) are shown. Figure S6. Metabotranscriptomic analysis of microarray and metabolite profiles in cells treated with 0.1 µg/µl MNPs@SiO2(RITC) for 12 h. (a) Lipid peroxidation and focal adhesion related genes and metabolites network were constructed algorithmically by IPA in 0.1 µg/µl MNPs@SiO2(RITC)-treated HEK293 cells and (b) prediction analysis for the network. Red and green areas indicate up- and downregulated genes, respectively. Orange and blue colours indicate activation and suppression, respectively. The lines indicate indirect (dotted) or direct (solid) relationship. Differentially expressed genes obtained from microarray data (&gt; 3-fold change) and disturbances in metabolic profile (&gt; 20% change) are shown. Figure S7. Metabotranscriptomic analysis of microarray and metabolite profile in cells treated with 1.0 µg/µl MNPs@SiO2(RITC) for 12 h. Lipid peroxidation and focal adhesion related genes and metabolites network were constructed algorithmically by IPA in 1.0 µg/µl MNPs@SiO2(RITC)-treated HEK293 cells. Red and green areas indicate up- and downregulated genes, respectively. Orange and blue colours indicate activation and suppression, respectively. The lines indicate indirect (dotted) or direct (solid) relationship. Differentially expressed genes obtained from microarray data (&gt; 3-fold change) and disturbances in metabolic profile (&gt; 20% change) are shown. Figure S8. Z-stack analysis for NPs treated HEK293 cells. The cells were treated with silica NPs and MNPs@SiO2(RITC) for 12 h. The locations of NPs were analysed with z-stack mode of confocal microscopy. Nucleus, blue; NPs, red; ubiquitin, green; lysosome, violet. Scale bar= 10 μm.