High-throughput single nucleotide variant discovery in E14 mouse embryonic stem cells provides a new reference genome assembly

•Identification of 2.7 × 10 E6 SNVs in mouse embryonic stem cell E14•About 15% of the identified variants are not annotated mouse SNVs.•Many of these SNVs are in common with the 129/Ola strain.•We generated a new genome assembly to be used as reference of E14 cell line.•The use of new E14 reference improves data mapping in next generation sequencing experiments.

Mouse E14 embryonic stem cells (ESCs) are a well-characterized and widespread used ESC line, often employed for genome-wide studies involving next generation sequencing analysis. More than 2 × 109 sequences made on Illumina platform derived from the genome of E14 ESCs were used to build a database of about 2.7 × 106 single nucleotide variants (SNVs). The identified variants are enriched in intergenic regions, but several thousands reside in gene exons and regulatory regions, such as promoters, enhancers, splicing sites and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of these cells. We created a new E14 genome assembly reference that increases the number of mapped reads of about 5%. We performed a Reduced Representation Bisulfite Sequencing on E14 ESCs and we obtained an increase of about 120,000 called CpGs and avoided about 20,000 wrong CpG calls with respect to the mm9 genome reference.