Gene expression analysis of wild-type and Beta-2-spectrin homozygous knockout (ß2SP-/-) mouse embryonic fibroblasts

Gene expression profiling was carried out in wild and ß2SP-/- (Sptbn1 -/-) mouse embryonic fibroblast (MEF) cells. Beta-2-spectrin (ß2SP) 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 TGFß signaling. In this study, we report a major role of the TGFß/Smad3 adaptor ß2-Spectrin in conserving genomic integrity from alcohol-induced DNA damage and describe a novel pathway that protects genomes from genotoxic stresses. Overall design: Whole-transcriptome RNA sequencing of wild-type and ß2SP knockout (ß2SP-/-) 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 ß2SP-/- MEF cells.

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Chen J, Yao ZX, Chen JS, Gi YJ, Muñoz NM, Kundra S, Herlong HF, Jeong YS, Goltsov A, Ohshiro K, Mistry NA, Zhang J, Su X, Choufani S, Mitra A, Li S, Mishra B, White J, Rashid A, Wang AY, Javle M, Davila M, Michaely P, Weksberg R, Hofstetter WL, Finegold MJ, Shay JW, Machida K, Tsukamoto H, Mishra L