Whole Genome Sequencing Pt1 Generation and characterization of a novel mouse model of Becker Muscular Dystrophy with a deletion of exons 52 to 55

Becker muscular dystrophy (BMD) is a rare X-linked recessive neuromuscular disorder, frequently caused by in-frame deletions in the DMD gene that result in the production of a truncated, yet functional, dystrophin protein. The consequences of BMD-causing in-frame deletions on the organism are difficult to predict, especially in regard to long-term prognosis. Here, we used CRISPR-Cas9 to generate a new Dmd Δ52-55 mouse model by deleting exons 52-55 in the Dmd gene, resulting in a BMD-like in-frame deletion. To delineate the long-term effects of this deletion, we studied these mice over 52 weeks by performing histology and echocardiography analyses and assessing motor functions. The dataset presented here shows the results of the Whole Genome Sequencing that was conducted to confirm the presence of the 52-55 deletion, and, thus, the generation of this new model. Due to size restrictions, this WGS dataset will be published on Zenodo in three parts. This first part contains the aligned and sorted bam file. 

Workflow: FASTQ files were first converted into unmapped BAM format using Picard FastqToSam. Subsequently, reads were aligned to a custom hybrid reference genome (GRCm38_68 combined with human hg38 sequences and additional vector constructs) using BWA MEM, followed by merging the aligned and unmapped reads with GATK's MergeBamAlignment. The resulting BAM files underwent duplicate marking using GATK MarkDuplicates tool to produce BAM files for downstream analysis. Data can be visualized using the Integrated Genome Viewer (IGV).