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Mus musculus

ABSTRACT: Gene expression analysis of wild-type and Beta-2-spectrin homozygous knockout (β2SP-/-) mouse embryonic fibroblasts

PROVIDER: PRJNA275639 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1806538_1.fastq.gz	Fastqsanger.gz
	SRR1806538_2.fastq.gz	Fastqsanger.gz
	SRR1806539_1.fastq.gz	Fastqsanger.gz
	SRR1806539_2.fastq.gz	Fastqsanger.gz

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Gene expression analysis of wild-type and Beta-2-spectrin homozygous knockout (Î²2SP-/-) mouse embryonic fibroblasts

Project description:Gene expression profiling was carried out in wild and Î²2SP-/- (Sptbn1 -/-) mouse embryonic fibroblast (MEF) cells. Beta-2-spectrin (Î²2SP) is a dynamic intracellular non-pleckstrin homology (PH)-domain protein that belongs to a family of polypeptides that have been implicated in conferring cell polarity. Spectrins have been linked to multiple signaling pathways, including cell cycle regulation, DNA repair and TGFÎ² signaling. In this study, we report a major role of the TGFÎ²/Smad3 adaptor Î²2-Spectrin in conserving genomic integrity from alcohol-induced DNA damage and describe a novel pathway that protects genomes from genotoxic stresses. Whole-transcriptome RNA sequencing of wild-type and Î²2SP knockout (Î²2SP-/-) mouse embryonic fibroblasts was carried out on an Illumina HiSeq 2000 sequencer. The raw data quality was assessed using a FastQC software. Adaptor presence was tested using Trimmomatic. The readings were then aligned to the NCBI mouse reference genome build 37.2 using the splice-aware aligner Tophat2 v2.0.10. Transcript quantification, normalization and assembly were carried out with Cufflinks. A gene model gtf file corresponding to the NCBI mouse reference genome build 37.2 was used in the quantification. Cuffdiff2, part of the Cufflinks suite of tools, was used to identify significant differences in gene expression profiles between the wild-type and Î²2SP-/- MEF cells.

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Project description:Gene expression profiling was carried out in six (wild type, β2SP+/-, β2SP-/-, SMAD3+/-, SMAD3-/- and β2SP+/-/ SMAD3+/-) different mouse knockout embryonic fibroblast (MEF) cells. Beta-2-spectrin (β2SP) is a dynamic intracellular non-pleckstrin homology (PH)-domain protein that belongs to a family of polypeptides that have been implicated in conferring cell polarity. Spectrins have been linked to multiple signaling pathways, including cell cycle regulation, DNA repair and TGFβ signaling. In this study, we report a major role of the TGFβ/Smad3 adaptor β2-Spectrin in conserving genomic integrity from alcohol-induced DNA damage and describe a novel pathway that protects genomes from genotoxic stresses. To determine the mechanism for the oncogenic switch, and whether it is related to the role of β2SP in TGF-β signaling transduction or secondary to its cytoskeletal functions, we analyzed disruption of two elements of the TGF-β pathway by generating double heterozygous Sptbn1+/−/Smad3+/− mice.

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