Confirmations of observations in the original paper so far

from my personal analysis on the published NGS data

FES1: 5kbp deletion in chromosome 3, but not in FES2
FES1: 17kbp deletion in chromosome 8, but not in FES2
FES1: Acr-GFP/CAG-GFP co-insertion as the transgene
FES1: about 20 copies of Acr promoters are inserted into the genome
FES1: transgene insertion in chromosome 3
FES1: duplication of a 20kbp region of chromosome 3 around the GFP insertion site
FES1: translocation of a 20kb region of chromosome 4 next to the GFP insertion site
FES1: a mosaic pattern of SNPs in the genome
FES1/FES2: FES1-specific 129 homo clusters of SNPs in chromosomes 6, 11, and 12
FLS3, 129GFP/ES, CTS1: 5kbp deletion in chromosome 3
FLS3, 129GFP/ES, CTS1: 17kbp deletion in chromosome 8
1290 SNP alleles that distinguish FES1 and FES2

STAP cell ChIP lysate: 4 deltions and 1 duplication in chromosomes


FES2 FLS3 CTS1 129GFP/ES STAP cell lysate

Things that are not reproduced by me so far

B6 homo clusters of SNPs in chromosomes 6, 11, and 12 of FES2

FES2 does not have 129 homo clusters that FES1 has. The corresponding regions of FES2 were shown to have B6 homo clusters in the original paper (pink regions in Fig. 1b, Ext. Fig. 1b and 1c). Strangely, these B6 homo culsters were also shown to exist in ntESG1 and ntESG2. In my analysis, however, there were no such regions and only seemed to have 129/B6 hetero regsions like the other parts of the genome. I confirmed my result by inspecting some of SNVs in the regions above in IGV for FES2.