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Next Generation Sequencing and Analysis of the Transcriptomes of RAW264.7 cells pretreated with PEP and PBS.

ABSTRACT: Next Generation Sequencing and Analysis of the Transcriptomes of RAW264.7 cells pretreated with PEP and PBS.

PROVIDER: PRJNA925439 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23118600_1.fastq.gz	Fastqsanger.gz
	SRR23118600_2.fastq.gz	Fastqsanger.gz
	SRR23118601_1.fastq.gz	Fastqsanger.gz
	SRR23118601_2.fastq.gz	Fastqsanger.gz
	SRR23118602_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing and Analysis of the Transcriptomes of RAW264.7 cells pretreated with PEP and PBS.

Project description:We demonstrate that phosphoenolpyruvate (PEP) generally inhibits viral infection in vitro and in vivo. In order to further explore whether PEP controls viral replication through a general mechanism such as enhancing innate response, and if not, what's the critical downstream target(s) of PEP, we performed RNA sequencing (RNA-seq) analysis on the RAW264.7 cells that were pretreated with 250 μM PEP or PBS for 2 hours, and then infected with or without vesicular stomatitis virus (VSV) for 8 hours.

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in 231 and Pep-E3 breast cancer cells by using NGS-derived breast cancer transcriptome profiling (RNA-seq). Methods: 231 and Pep-E3 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of 231 and Pep-E3 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 NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

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