Custom reference transcriptome for transgenic mouse genome based on mm10

Reads were aligned to this custom reference genome, which was created based on the mouse mm10 reference genome v1.2.0 provided by 10x Genomics. Firstly, sequences for transgenes Sgcb1a1 (3’ of ER + 130 bp linker + 3’ UTR of Scgb1a1), Sftpc (rtTA-M2 coding sequence) and DTA were added to the reference genome FASTA file. Subsequently, the endogenous Esr1 (genomic position Chr10:4611989-5005614) and 3’ UTR of Scgb1a1 (genomic position Chr19:9083642-9083739) were masked from the genome. Then, three lines corresponding to the newly-added transgene sequences were added to the reference genome GTF file. Lastly, Cell Ranger was used to create the reference genome package from the modified FASTA and GTF files.