PLX176135

GSE149647: The effect of active YAP in neonatal heart of Xin knockout mice

• Organsim mouse
• Type RNASEQ
• Target gene
• Project ARCHS4

Purpose: The goals of this study are 1) to define the transcriptome changes in the heart in the absence of intercalated-disc protein Xin, and 2) to define the effect of active Yap overexpression on the cardiac transcriptome in the absence of Xin.; Methods: Total RNA from heart apex of postnatal day (P) 7.5 Xin KO or WT mice were profiled by bulk-RNA sequencing (50bp SE). Total RNA from heart apex of P7.5 Xin KO or WT mice injected with AAV9 carrying cardiac troponin T promoter driven active Yap (S127A) or GFP (control) at P1 were profiled by bulk-RNA sequencing (150bp PE). FASTQ files were extracted, and the TruSeq sequencing adapters and low-quality reads were removed from FASTQ files with Cutadapt v.2.3. The cleaned FASTQ files were quality checked using FastQC (Babraham Bioinformatics), then aligned to the mouse genome (Esembl GRCm38 genome obtained from GENCODE) using HISAT2 (v.2.1.0). Subsequently, transcript assembly was performed using StringTie (v.1.3.4) with the annotated transcriptome as a reference. The assembled transcriptomes were quantified using prepDE.py script provided by the StringTie developer to generate gene matrix files. EdgeR (v.3.26.1) was used to compute Counts Per Million (CPM) as a normalized measurement for gene expression. Differentially expressed genes were tested using the Fishers exact test, and multiplicity correction is performed with the Benjamini-Hochberg method on the p-values, to control the false discovery rate (FDR).; Results: We find that Xin knockout heart have changes on the transcriptome with hallmark of decrease proliferation etc. and subsets of the transcriptome alteration induced by the absence of Xin could be rescued by overexpressing active Yap in the neonatal mice. SOURCE: Da-Zhi Wang (Da-Zhi.Wang@childrens.harvard.edu) - Boston Children's Hospital