Material dispersions were prepared in glass tubes as stock dispersions of 1 mg/ml in cell growth medium (BEGM, Clonetics, Walkerwille, MD, USA) with 0.6 mg/ml of bovine serum albumin (BSA; Sigma-Aldrich, Steinheim, Germany) and sonicated for 20 min at 37 °C in a bath sonicator (Branson 2200, 40 kHz). The freshly prepared and sonicated stock dispersions were further serially diluted to obtain the final dispersions of 0.25, 2 and 10 μg/cm2 (corresponding to 2, 16 and 80 μg/ml), sonicated again and directly applied onto the cells.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using 0.5 ml TRIZOL (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions and purified using miRNeasy® Mini Kits (kit 217004, Qiagen, miRNeasy Mini Handbook).
Label
biotin
Label protocol
Sample preparation, hybridisation, washing, staining and scanning of Agilent Human miRNA Microarrays (8x60K) were conducted according to the manufacturers’ standard manuals (the Agilent miRNA Microarray System Manual)
Hybridization protocol
Sample preparation, hybridisation, washing, staining and scanning of Agilent Human miRNA Microarrays (8x60K) were conducted according to the manufacturers’ standard manuals (the Agilent miRNA Microarray System Manual)
Scan protocol
Sample preparation, hybridisation, washing, staining and scanning of Agilent Human miRNA Microarrays (8x60K) were conducted according to the manufacturers’ standard manuals (the Agilent miRNA Microarray System Manual)
Data processing
Foreground and background intensity, spot saturation, spot mean-median ratio and level above background was evaluated using an in-house developed pipeline in R. Pre-processing of the miRNA data was performed by the R/Bioconductor package AgiMicroRNA. Total Gene Signals were quantile-normalized, log2 transformed and filtered on isGeneDetected flag according to the script.
