Truseq preparation kits

Two samples (USCF134; USCF136) were selected for whole genome sequencing on the Illumina HiSeq 2000 (Illumina, San Diego, CA). Tissue samples were taken from muscle of the affected pups and digested overnight with Proteinase K. Genomic DNA was extracted with the Nucleon BACC 2 Genomic DNA Extraction Kit (GE Healthcare). Paired-end libraries were prepared with the Illumina TruSeq preparation kits and sequenced according to vendor instructions by the Ramaciotti Centre at the University of New South Wales, Kensington. Libraries were barcoded and both samples sequenced in a single lane of the sequencing machine.

Total RNA from mouse heart left ventricle was prepared by Trizol extraction from flash-frozen tissue. Six (6) biological replicates were used for each of rAAV6-blank, rAAV6-PLCβ1a and rAAV6-PLCβ1b conditions. Ribosomal RNA depletion along with RNA fragmentation and conversion to paired-end, strand-specific Illumina sequencing libraries were performed with Illumina TruSeq preparation kits. Sequencing reads of 76 nt in length were obtained from multiplexed libraries on an Illumina NextSeq instrument at the Ramaciotti Centre for Genomics, Sydney, Australia with (3.02 ± 0.11) * 10⁷ paired reads per heart (mean ± SEM). Reads were aligned to the mouse transcriptome represented in the Illumina iGenomes mm10 UCSC release using Tophat [21 (link)], achieving a read depth of (1.84 ± 0.07) * 10⁷ paired reads per heart (mean ± SEM); this represents a mean alignment to the transcriptome of 61%. All mRNA-sequencing reads and transcriptome-aligned read counts have been deposited in the NCBI GEO with accession number GSE73909.