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RNA-seq data from NSCs and tumorspheres generated using the RCAS/TVA-CRISPR/Cas9 system

ABSTRACT: RNA-seq data from NSCs and tumorspheres generated using the RCAS/TVA-CRISPR/Cas9 system

PROVIDER: PRJNA434303 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6739720_1.fastq.gz	Fastqsanger.gz
	SRR6739720_2.fastq.gz	Fastqsanger.gz
	SRR6739730_1.fastq.gz	Fastqsanger.gz
	SRR6739730_2.fastq.gz	Fastqsanger.gz
	SRR6739721_1.fastq.gz	Fastqsanger.gz

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RNA-seq data from NSCs and tumorspheres generated using the RCAS/TVA-CRISPR/Cas9 system

Project description:It has been gradually established that the vast majority of human tumors are extraordinarily heterogeneous at a genetic level. To accurately recapitulate this complexity, it is now evident that in vivo animal models of cancers will require to recreate not just a handful of simple genetic alterations, but possibly dozens and increasingly intricate. Here, we have combined the RCAS/TVA system with the CRISPR/Cas9 genome editing tools for precise modelling of human tumors. We show that somatic deletion in neural stem cells (NSCs) of a variety of known tumor suppressor genes (Trp53, Cdkn2a and Pten), in combination with the expression of an oncogene driver, leads to high-grade glioma formation. Moreover, by simultaneous delivery of pairs of guide RNAs (gRNAs) we generated different gene fusions, either by chromosomal deletion (Bcan-Ntrk1) or by chromosomal translocation (Myb-Qk), and we show that they have transforming potential in vivo and in vitro.

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Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB driven gliomas

Project description:Here we describe the use of a high-throughput pipeline coupled to the commonly used tissue-specific retroviral RCAS-TVA mouse tumor model system. Utilizing next generation sequencing, we show that retroviral integration sites can be reproducibly detected in malignant stem cell lines generated from RCAS-PDGFB-driven glioma biopsies.

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Expression data from RCAS PDGFB/Nestin tv-A glioma cells within Ptprd+/+p16-/- (n=2), Ptprd+/-p16-/- (n=2), and Ptrpd-/-p16-/- (n=3) mice.

Project description:PTPRD is a tumor suppressor of glioma that is frequently co-deleted with CDKN2A/p16. We show that Ptprd and p16 cooperate to promote gliomagenesis in the RCAS PDGFB / Nestin tv-A glioma mouse model. We found unique gene expression changes within tumor cells of Ptprd+/-p16-/- vs. Ptprd+/+p16-/- and Ptprd-/-p16-/- tumor cells. Neonatal mice were injected with RCAS PDGFB GFP. At symptoms, or at 12 weeks post injection, GFP+DAPI- tumor cells were sorted for RNA extraction and hybridization on Affymetrix microarrays. The mouse strain used was a mixed background of C57/BL6 and FVB/N. Ptprd mice were from Uetani et al. 2000 and p16/Nestin-tvA mice were from Tchouganouva et al. 2007.

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Effect of ATRX deficiency on gene expression of RCAS-nTva derived murine gliomas [RNA-seq: ATRX_Immuno_cell_line]

Project description:To investigate the impact of ATRX loss on tumor microenvironment we generated ATRX-intact and -deficient tumors in immune competent mice with the RCA-nTva system. Mice were injected with a tumorigenic RCAS construct (PDGFa and shTP53) and an RCAS bearing CRE recombinase. This was performed in mice that were ATRX wt and ATRX floxed. Tumors were then harvested, processed, and cell lines were generated and cultured for downstream analysis.

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Effect of trans-vaccenic acid(TVA) diet on 16S ribosomal RNA (rRNA) expression of mouse gut microbiome

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