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. Author manuscript; available in PMC: 2019 Mar 1.
Published in final edited form as: Nat Biotechnol. 2018 Jul 16;36(8):765–771. doi: 10.1038/nbt.4192

Figure 3. Analysis of Cas9 editing at the autosomal Cd9 locus in mouse ES cells.

Figure 3

Experimental setup is analogous to the PigA experiment in Fig. 1A. A mouse ES cell line derived from an F1 cross between Mus musculus castaneus (CAST) and Mus musculus (BL6) was used. (A) Positions of primer pairs and gRNAs (Tables S1 and S6). Genomic position is given with respect to the GRCm38 reference genome. (B) Examples of Cd9 editing revealed by antibody staining, for two gRNAs and one control (Table S1; N=7 biologically independent cell cultures). (C) PacBio alleles derived from Cd9 positive, mixed (bimodal) and negative, individually sequenced single cell clones, displayed as a pileup. Display conventions as in Fig. 2. N=1. (D) Recombinant alleles. Two of the sequenced single cell clones contained alleles indicative of a cross over event between the homologous chromosomes. Red vertical bars in CAST allele (grey bar) indicate positions of sequence divergence from the BL6 reference genome (black bar), dotted black line indicates missing sequence (deletion), thin black line indicates an intron. LOH – loss of heterozygosity.