Data for: "PEGylation-dependent metabolic rewiring of macrophages with silk fibroin nanoparticles"

Silk fibroin nanoparticles were produced using a dedicated method. The study aimed to characterise the effects of silk fibroin nanoparticle PEGylation and concentration on the activation of RAW264.7 macrophages. Physical properties of silk fibroin nanoparticles were characterised by dynamic light scattering (DLS) and scanning electron microscopy (SEM). Macrophage inflammatory phenotype was characterised using a combination of in vitro assays, measured using a PolarSTAR Omega plate reader or BD FACSCanto flow cytometer. The metabolic profiles of macrophages were characterised using H1 nuclear magnetic resonance (NMR). Nanoparticle surface binding, endocytosis and intracellular trafficking were measured by live confocal microscopy.

Equipment used in production of data:
- Zetasizer: Zetasizer Nano-ZS (Malvern Instrument, Worcestershire, U.K.)
- Flow cytometer: BD FACSCanto (Becton Dickinson, San Jose, CA, USA)
- Confocal Microscope: Leica TCS-SP5 (Leica Microsystems GmbH, Wetzlar, Germany)
- Plate reader: PolarSTAR Omega (BMG Labtech, Ortenberg, Germany)
- FTIR spectrophotometer: TENSOR II FTIR spectrometer, Bruker Optik GmbH, Ettlingen, Germany
- FACSDiva software: BD FACSDiva v6.3.1 (Becton Dickinson, San Jose, CA, USA)
- Flow Jo software: FlowJo v10.1 (TreeStar, San Carlos, CA, USA)
- ImageJ software: ImageJ v1.51k 1 (National Institutes of Health, Bethesda, MD, USA)

All datasets provided as zipped folders assigned to each figure.

Figure 1: PEGylating, sizing and zeta potential of silk nanoparticles
- Data provided within Figure 1 folder:
(i) "NP SEMs" - Nanoparticle SEM images
(ii) "FTIR Data" - FTIR analyses of silk nanoparticles
(iii) "Particle DLS Data" - Particle size, PDI and zeta potential measurements
(iv) "Figure cartoon" - cartoon generated to represent silk nanoparticle structures

Figure 2: Cellular response to silk fibroin nanoparticles.
- Data provided within Figure 2 folder:
(i) "MTTs" - All MTT cytotoxicity assay data
(ii) "LDH Assay" - All LDH membrane integrity assay data
(iii) "SEMs" - All SEM data of silk fibroin nanoparticles and macrophages

Figure 3: Confocal imaging of silk nanoparticle co-localisation with lysosomes
- Data provided within Figure 3 folder:
(i) "PEGSNP" images analysed for PEG-SNP treated RAW264.7 cells
(ii) "SNP" images analysed for SNP treated RAW264.7 cells
(iii) "Image Manders Tests.xlsx" - results of Manders tests on images
(iv) "All ROIs.zip" - all Regions of Interest (ROIs) used for figure formatting and Manders testing

Figure 4:
- Data provided within Figure 4 folder:
(i) "ROS Study" - FCS files as .wsp file. All raw data as .xls file. Analysed data as .pzfx file.
(ii) "Antioxidant Assay_Jan2019.pzfx" - all antioxidant assay data
(iii) "TNF-a ELISA 10-01-18.pzfx" - all TNF-a ELISA data
(iv) "16-01-18_Griess Assay_RAW264.7_SNP_P-SNP.pzfx" - all Griess Assay data
(v) "Proteome Arrays" Raw data as .xlsx file. Heatmaps as .pzfx file.