Verification of CRISPR editing and finding transgenic inserts by Xdrop™ Indirect sequence capture followed by short- and long- read sequencing
Two reconstructed APOE reference loci on GRCh38.p13 Chr19:44,900,000-44,920,000 including corresponding pEasy Flox fragments of 3.4 kb and 4.4 kb. A reconstructed Pax8-CreERT2 reference loci on GRCm38.p6 chr1: 93570239-93676772.
Steps to reproduce
Xdrop enrichment for indirect sequence capture regions surrounding CRISPR edited sites in cell lines and transgene insertion in a mouse line. Illumina and Oxford Nanopore sequencing of the captured region made it possible to understand the consequences of the CRISPR edit and built new reference sequences. For the transgenic mouse the data allowed for identification of the insertion site and to find the deletion caused by the insertion, based on this a new reference sequence was also built.