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Transcription profile of intracellular H37Ra of bEnd.3 and Raw 264.7 cells

ABSTRACT: Transcription profile of intracellular H37Ra of bEnd.3 and Raw 264.7 cells

PROVIDER: PRJNA680950 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13150655_1.fastq.gz	Fastqsanger.gz
	SRR13150655_2.fastq.gz	Fastqsanger.gz
	SRR13150656_1.fastq.gz	Fastqsanger.gz
	SRR13150656_2.fastq.gz	Fastqsanger.gz
	SRR13150657_1.fastq.gz	Fastqsanger.gz

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Transcription profile of intracellular H37Ra of bEnd.3 and Raw 264.7 cells

Project description:Transcription profile of intracellular H37Ra of bEnd.3 and Raw 264.7 cells 3 d.p.i

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Expression data from RAW 264.7 macrophage

Project description:IFNg is a pro-inflammatory and pro-atherogenic cytokine that leads to macrophage activation. Adenosine has well-documented anti-inflammatory properties. We used microarrays to compare the global gene expression profile in mouse macrophages stimulated with IFNg alone and those cells treated with IFNg and adenosine. We determined that adenosine suppressed the expression of many IFNg-regulated pro-inflammatory cytokines, chemokines, and other pro-atherogenic genes. Keywords: treatment response RAW 264.7 cells were treated for 4 hours with either IFNg or IFNg plus adenosine. Following treatment, total RNA was extracted and treatment groups were pooled from 2 separate experiments for hybridization of Affymetrix microarrays.

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Next Generation Sequencing of Wild Type and Hnrnpul1-/- RAW 264.7 Cells Transcriptomes

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.

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