GSE185830
RNA Sequencing of BV2 cells stimulated by sTREM-1
Purpose:  The goals of this study are to compare the transcriptome of  BV2 cells stimulated with or without sTREM-1, explore its effect on the phenotype and function of BV2 cells, and explore potential signaling pathways. Methods: BV2 cells were incubated with or without sTREM-1 recombinant protein (1ug/mL) for 6 h, then the mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. Results: Sequencing libraries were generated using the NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) and sequenced on an Illumina platform. Paired-end reads were then generated and evaluated for quality control. Clean raw data with high quality were aligned to the reference genome using Spliced ??Transcripts Alignment to a Reference (STAR) software. For quantification, FeatureCouts was used to count the read numbers mapped of each gene, 17047 transcripts were identified. Differential expression analysis between two groups was performed using the Edge R package. Genes with an adjusted RNAs with P?<?0.05 and |log2FC |?>?1 were identified as differentially expressed. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to sTREM-1 function. Gene ontologies (GO) Analyses were conducted to assess biological processes, molecular functions, and cellular components. Conclusions: Our study represents the detailed analysis of BV2 cells transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that BV2 cells are activated after sTREM-1 recombinant protein stimulation, and the phagocytic function is enhanced. Overall design: Stimulate BV2 cells with sTREM-1 in vitro, and explore mRNA profiles through RNA-Seq.