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Effect of Gsdmc knockdown in murine KPC cells transcriptome

ABSTRACT: Effect of Gsdmc knockdown in murine KPC cells transcriptome

PROVIDER: PRJNA1051955 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27196900_1.fastq.gz	Fastqsanger.gz
	SRR27196900_2.fastq.gz	Fastqsanger.gz
	SRR27196901_1.fastq.gz	Fastqsanger.gz
	SRR27196901_2.fastq.gz	Fastqsanger.gz
	SRR27196902_1.fastq.gz	Fastqsanger.gz

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Effect of Gsdmc knockdown in murine KPC cells transcriptome

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Project description:Recently, Bailey et al (2016, Nature) defined four subtypes of pancreatic cancer that are associated with distinct histopathological characteristics and differential survival, namely, Squamous, Pancreatic Progenitor, Immunogenic, and ADEX (Aberrantly Differentiated Endocrine eXocrine). We set out to assess by RNASeq whether loss of CXCR2 was significantly associated with a specific PDAC subtype. Pancreatic tumors were harvested from KPC or KPC Cxcr2-/- mice at endpoint (n=5 v 5), RNA prepared, and RNASeq analysis carried out. Reads were analysed using the bcbio-nextgen framework (https://bcbio-nextgen.readthedocs.org/en/latest/). After quality control and adaptor trimming, reads were aligned to the mouse genome build (UCSC mouse mm10) using STAR. Counts for known genes were generated using the function featureCounts in the R/Bioconductor package \Rsubread\. The R/Bioconductor package edgeR was used to identify differentially expressed genes.

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