title: HiSeq X Ten paired end sequencing; Wild type mouse short read WGS
library_construction_protocol: Sequencing libraries were prepared using Illumina SeqLab specific TruSeq Nano High Throughput library preparation kits in conjunction with the Hamilton MicroLab STAR and Clarity LIMS X Edition. The samples were normalised to the concentration and volume required for the Illumina TruSeq Nano library preparation kits, then sheared to a 450bp mean insert size using a Covaris LE220 focused-ultrasonicator. The inserts were ligated with blunt ended, A- tailed, size selected, TruSeq adapters and enriched using 8 cycles of PCR amplification. The libraries were evaluated for mean peak size and quantity using the Caliper GX Touch with a HT DNA 1k/12K/HI SENS LabChip and HT DNA HI SENS Reagent Kit, and normalised to 5nM using the GX data and the actual concentration established using a Roche LightCycler 480 and a Kapa Illumina Library Quantification kit and Standards.  The libraries were normalised, denatured, and pooled in eights for clustering and sequencing using a Hamilton MicroLab STAR with Genologics Clarity LIMS X Edition. Libraries were clustered onto HiSeqX Flow cell v2.5 on cBot2s and the clustered flow cell is transferred to a HiSeqX for sequencing using a HiSeqX Ten Reagent kit v2.5. Demultiplexing was performed using bcl2fastq 2.17.1.14, allowing 1 mismatch when assigning reads to barcodes.