RNAseq analysis of silica coated magnetic nanoparticles treated BV2 cells

We report the gene expression profile in BV2 murine microglia cell line after treatment of silica coated magnetic nanoparticles with low dose (0.01 µg/µl) and high dose (0.1 µg/µl) for 12 h. To analyze the changes of gene expression after treatment with silica-coated-magnetic nanoparticles containing the rhodamine B isothiocyanate dye [MNPs@SiO2(RITC)] in BV2 cells, BV2 cells were treated with 0.01 and 0.1 µg/µl of MNPs@SiO2(RITC) for 12 h, lysed, and total RNA was isolated with TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA). RNA quality was analyzed by rRNA band integrity on an Agilent RNA 6000 Nano kit (Agilent Technologies, CA). cDNA library was constructed from 1 µg of total RNA. Magnetic beads conjugated with Oligo (dT) were used to enrich poly A tailed mRNA. Purified mRNAs were fragmented into short fragments, and double-stranded cDNAs were synthesized. The cDNAs were modified with end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). cDNA fragments were purified with BluePippin (Sage Science, MA) and amplified by PCR. The cDNA library size and quality were determined with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA). The library was sequenced using an Illumina HiSeq2500 sequencer (Illumina, CA).