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Poly-A transcriptome changes in mouse embryonic fibroblasts (MEFs) after spontaneous immortalization

ABSTRACT: Poly-A transcriptome changes in mouse embryonic fibroblasts (MEFs) after spontaneous immortalization

PROVIDER: PRJNA1107188 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28878882_1.fastq.gz	Fastqsanger.gz
	SRR28878882_2.fastq.gz	Fastqsanger.gz
	SRR28878883_1.fastq.gz	Fastqsanger.gz
	SRR28878883_2.fastq.gz	Fastqsanger.gz
	SRR28878884_1.fastq.gz	Fastqsanger.gz

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Poly-A transcriptome changes in mouse embryonic fibroblasts (MEFs) after spontaneous immortalization

Project description:In our study, we characterized the changes in poly-A gene expression atributed to the process of spontaneous immortalization using a mouse embryonic fibroblasts (MEF) model. Primary MEFs were established, serially passaged and spontaneously immortalized using a modified 3T3 NIH protocol. We then performed gene expression profiling analysis using RNA-seq data of 3 different clones at two time points (primary and immortalized).

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Project description:Mus musculus strain:mouse embryonic fibroblasts (MEFs) | isolate:MEFs | breed:MEFs | cultivar:Mus musculus Raw sequence reads

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Project description:Using a supercritical fluid chromatography-mass spectrometry (SFC-MS)-based methodology, we quantified phosphoinositides (PIPs) species in mouse embryonic fibroblasts (MEFs) from WT or FIP200 KO mice during autophagosome formation.

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Viral integration promotes SV40T-induced immortalization by disturbing the expression of DNA/chromosome- and ECM-associated functional genes

Project description:Lentivirus containing simian virus 40 large T antigen (SV40T) is routinely used to induce cell immortalization. However, the roles of viral integration itself in this progress is still controversial. Here, we transformed primary mouse embryonic fibroblasts (MEFs) with SV40T lentivirus and studied the roles of viral integration in the immortalization using RNA-seq and whole genome sequencing (WGS). During the immortalization, differentially expressed genes (DGEs) are enriched in viral infection and several diverse activities. However, DEGs between immortalized and aging cells are significantly enriched in DNA/chromosome- and extracellular matrix (ECM)-associated activities. Gene regulatory network (GRN) analysis shows that although p53 is a key regulatory factor, many other transcription factors also play critical roles in the process, like STAT1. Of these DEGs, 32 genes have viral integration in their coding and/or regulatory regions. Our findings suggest that viral integration may promote SV40T-mediated immortalization by disturbing the expression of DNA/chromosome- and ECM-associated genes.

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