Project description:We focused on how mica fine particle influences macrophage activities. We analyzed altered transcription in RAW 264.7 cells at 0, 12, and 48 h following the stimulation with 100 M-BM-5g/mL of mica fine particles.
Project description:We report the application of RNA sequencing to determine the transcriptional response of primary bone marrow macorphages and murine macrophage Raw 264.7 cells in response to stimulation with LPS/IFNgamma(M1) or IL-4 (M2) stimulation conditions
Project description:Purpose: The goal of this study is to compare NGS-derived wild type and Hnrnpul1 knockout (Hnrnpul1-/-) RAW 264.7 cells transcriptomes with or without LPS stimulation. Methods: Sequancing was performed by Novogene China Co. Ltd. RNA profiles of wild type and Hnrnpul1-/- RAW 264.7 cells as well as LPS stimulated (10 h) wild type and Hnrnpul1-/- RAW 264.7 cells were generated by deep sequencing using Illumina Novaseq 6000. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Method of TMM was used to normalize the readcount. Negative binomial distribution model was used to calculate the P value, and FDR was calculated by the method of Benjaminiand Hochberg. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (GRCm38/mm10). Comparing to wild type RAW 264.7 cells, 237 genes were up-regulated and 181 genes were down-regulated in Hnrnpul1-/- cells. At 10 h following LPS stimulation, 341 genes were up-regulated and 288 genes were down-regulated in Hnrnpul1-/- cells. Genes were pre-ranked according to log2FoldChange(KO/WT) followed by GSEA and 6 gene sets were significantly enriched. Significantly differential genes were undergone GO analysis (biological process) and biological process including cell-cell adhesion, positive regulation of cell activation and regulation of response to external stimulus were enriched. Conclusions: Lacking Hnrnpul1 promotes the expression of inflammatory cytokines in LPS stimulated RAW 264.7 cells.
Project description:The involvement of m6A modification in macrophage activation has been validated in our study that the expression of TNF-α in Mettl3-depleted Raw 264.7 cells stimulated with LPS were markedly reduced in comparison to control cells. To further explore the biological effects of m6A deficiency macrophages, we performed RNA sequencing analysis of Mettl3-KO and WT control Raw 264.7 cells upon LPS treatment. The GO enrichment analysis documented that the downregulated transcripts in Mettl3-KO Raw 264.7 cells were enriched in innate immune response related to defense and external stimulus. Notably, transcripts of the downstream components of the TLR4 signaling pathway, such as proinflammatory cytokines (Tnf-α, Il-6, Il-1β, Il-18,and Il-23) and co-stimulation molecules (Cd86), were downregulated in Mettl3-deficient cells, suggesting that METTL3 has a critical function in controlling the innate immune response of Raw 264.7 macrophages.
Project description:To investigate the extent to which macrophages respond to Salmonella infection, researchers infected RAW 264.7 macrophages with Salmonella enterica serotype Typhimurium and analyzed macrophage proteins at various time points following infection by using a global proteomic approach.
Project description:We focused on whether transposon mutagenesis in Brucella abortus could induce difference in the trascriptional responses of RAW 264.7 cell infection model compared to the wild strain infected RAW 264.7 cells. The function of genes in Brucella abortus was analyzed through the identified differences in gene expression between RAW 264.7 cell infected with wild and mutant strains. We analyzed altered transcription in RAW 264.7 cells at 0, 6, 12, and 24 h following the infection with 10 MOI of Brucella abortus wild and mutant strains.
Project description:We performed ChIP-seq with antibody targeting hnRNP UL1 at 0, 4h and 10h following LPS stimulation in RAW 264.7 cells. NGS and data analysis were done by Novogen China Co. Ltd. We found that hnRNP UL1 binds to chromatin DNA broadly and dynamically during inflammatory response. hnRNP UL1 binds to genes' promoter mainly. And NF-κB binding sites (κB sites) were significantly enriched in the motifs bound by hnRNP UL1.
Project description:Edema toxin (EdTx), which is a combination of edema factor and a binding moiety (protective antigen), is produced by Bacillus anthracis, the etiological agent of anthrax. EdTx is an adenylyl cyclase enzyme that converts adenosine triphosphate to adenosine-3',5'-monophosphate, resulting in interstitial edema seen in anthrax patients. We used GeneChip analysis to examine global transcriptional profiles of EdTx-treated RAW 264.7 murine macrophage-like cells at 3 and 6 hr. Experiment Overall Design: RAW 264.7 cells were treated with EdTx (2.5 µg/ml of protective antigen and 0.625 µg/ml of Edema factor), PA (2.5 µg/ml), or LPS (1 ng/mL) for 0, 3, and 6 hr. Each experiment was performed in triplicate, generating a total of 21 arrays (biological replciates).
