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Next Generation Sequencing Facilitates Quantitative Analysis of CAFR and CAFS Transcriptomes in pancreatic cancer

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of CAFR and CAFS Transcriptomes in pancreatic cancer

PROVIDER: PRJNA793781 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17408173_1.fastq.gz	Fastqsanger.gz
	SRR17408173_2.fastq.gz	Fastqsanger.gz
	SRR17408174_1.fastq.gz	Fastqsanger.gz
	SRR17408174_2.fastq.gz	Fastqsanger.gz
	SRR17408175_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of CAFR and CAFS Transcriptomes in pancreatic cancer

Project description:We extracted primary CAFs from the tumor tissue of chemoresistant and chemosensitive pancreatic cancer patients (namely CAFR and CAFS). The Goal of this study is to compare the transcriptomes difference between CAFR and CAFS. And we come to a conclusion that CAFR is possessed of a iCAF phenotype.

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Project description:Purpose: The goals of this study are to compare EG7 - CAFs (cancer-associated fibroblasts) and MSCs (mesenchymal stem cells) transcriptome profiling (RNA-seq) generated from Next-generation Sequencing (NGS) to perform optimal high-throughput data analysis Methods: mRNA profiles of CAFs were purified from EG7 tumor bearing mice and early passage (p6) murine MSCs purchased from Cyagen were cultured in DMEM for no more than 2 passages were generated by deep sequencing, in triplicate, using Illumina HiSeq 3000. The sequence reads that passed quality filters were analyzed at the transcript isoform level TopHat followed by Cufflinks Results: Comparative high throughput RNA-sequencing (seq) analysis of purified EG7-CAFs and the early passage murine MSCs, which are thought to be precursors for some CAFs and used as the control for normal mesenchymal cells, by using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 11,839 transcripts with TopHat workflow. Approximately 1584 of the transcripts showed differential expression between the EG7 - CAFs and MSCs, with a fold change ≥ 2 and p value <0.01 Conclusions: Our results clearly support the notion that CAFs are transcriptionally different from MSCs in various pathways and biological processes associated with immune modulation, inflammation, hypoxia, and activation of oncogenic pathways

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