学術界の人たちがひたすら沈黙する社会的な現象も、ESねつ造は単なる印象操作にすぎなかったことを示すものです。

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SUPPLEMENTARY INFORMATION doi:10.1038/nature15366
　
Supplementary Methods 
　
Materials 
All samples examined in this investigation had been stored at the laboratories of the original papers’ authors1,2 , except for FES1, FES2, ntES1 and e<n>tES2 cells (given by H. Ohta) and Acr/cag-GFP mice (from the frozen embryonic stocks at the CDB). 
　
Cell culture 
STAP stem cell lines (FLS3, 4, GLS1, 11, and AC129-1,2) and FI stem cells (CTS1, 11) were cultured with mouse embryonic fibroblast feeder cells treated with Mitomycin C in GMEM supplemented with 10% FCS, 1x sodium pyruvate, 1x non-essential amino acids, 10^-4 M 2-mercaptoethanol and 1000 U/ml LIF.FI stem cells were cultured with mouse embryonic fibroblast feeder cells treated with Mitomycin C in GMEM supplemented with 20% FCS, 1x sodium pyruvate, 1x non-essential amino acids, 10^-4 M 2-mercaptoethanol, 2 µg/ml heparin and 50 ng/ml human FGF4. The remaining cell lines were cultured using the 2I-LIF method3 with 10% FBS.
　
Whole-genome sequencing and SNP identification
We used the TruSeq DNA PCR-Free LT Sample Prep Kit for sequencing library construction using a standard protocol. The insert size of the STAP cell lysate sample is 350 bp and the other 14 samples are 550 bp each. We performed paired-end 150 bp sequencing for each DNA sample using 2 flow cells in the rapid-run mode of a HiSeq 2500 sequencer. We aligned paired-end sequence tags to the GRCm38 (mm10) mouse reference genome using BWA software4 (ver. 0.7.10) with “-n 0.02” option for the bwa aln command and “-a 2000000” option for the bwa sampe command. Raw data are available at DDBJ DRA (accession: DRA002862) (http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=DRA002862). 
　
After filtering properly mapped tags and then removing PCR duplication with SAMtools (ver. 0.1.19), we identified SNPs from the aligned sequence data using SAMtools Mpileup and BCFtools (ver. 0.1.19) with default options. We also identified reliable SNVs including heterozygous alleles from aligned sequence data that satisfied the following criteria using SAMtools Mpileup after filtering the properly mapped tags. (1) Sequence coverage > 20. (2) At least 25% of reads supported alternative alleles that differed from the B6 reference sequence. For comparison to 129/Sv SNPs, we used commonly called SNPs in 129P2/OlaHsd (EMBL ENA: ERP000034), 129S1/SvImJ (EMBL ENA: ERS076385), and 129S5SvEvBrd (EMBL ENA: ERP000036) but not called in C57BL/6NJ (EMBL ENA: ERS076384) provided by the Wellcome Trust Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/). 
　
Identification of gfp insertion sites 
We mapped the reads to gfp sequences and extracted mate-pairs for which only one end was mapped to the gfp sequence using BWA. The extracted reads were mapped to the human<→mouse> genome. We manually inspected the mate-pairs bridging between gfp and mouse genome sequences using IGV<5> and determined the exact positions of insertion sites supported by multiple mate-pairs. 
　
Detection of long deletions and duplications
We used SVDetect with a "linking" option to find long deletions and duplications as potential signatures that can identify identical samples<6>. The detected candidates were filtered using "filtering" and "links2compare" options to obtain reliable structural changes and were manually inspected and validated by PCR and Sanger sequencing. 
　
Quantitative PCR of teratoma samples 
Genomic DNA was extracted using a QIAGEN QIAamp DNA FFPE Tissue kit (Qiagen) from 10 to 20 sections 5µm thick that had been sliced out of paraffin blocks. Genomic DNA samples were prepared from the STAP cell teratoma block in duplicate (2.2 µg and 6.1 µg). Newly prepared solutions, PCR primers and apparatus were used for the second isolation. All PCR primers for quantitative PCR were designed to be less than 100 bp in length so that fragmented DNAs in the fixed samples were efficiently amplified. Quantitative PCR was performed with FastStart Universal SYBR Green Master Mix (Roche) in a TAKARA TP 860. The degree of PCR amplification was quantified relative to that of the Il2 gene as a standard using the ΔΔCt method. Initially, we detected gfp with two different primer sets to roughly estimate its relative copy number compared with two copies of the Il2 gene/genome, followed by the determination of the gfp transgene type using PCR primers that detect the junction between the Acrosin gene promoter (and the Oct4-promoter) and the gfp gene. The amplification efficiency of primer pairs for Acr-gfp and Oct4-gfp relative to that for Il2 gene was not quantified, but the copy number of Acr-gfp in FLS4 and Oct4-gfp in GLS13 relative to the Il2 gene coincided with the values determined by WGS (20–24 copies vs. approximately 28 copies, respectively), suggesting that the amplification efficiency of individual PCR primers was within a permissible range.
　
Antibody staining of teratoma samples 
Paraffin sections were prepared from the paraffin block of the teratoma samples after slicing approximately 100 x 5 μm sections for DNA extraction and treated according to a standard protocol for immunostaining. Chick anti-GFP antibody (Abes, GFP-1020) was used at a 1/500 dilution. 
　
PCR primers
The sequences of the PCR primers used in this investigation are available upon request. 
　
We thank N. Kondo and the Genome Network Analysis Support Facility (GeNAS) at the RIKEN Center for Life Science Technologies for WGS. We also thank T. Endo, H. Ohta, S. Hayashi, H. Kiyonari, S. Kuraku, C. Kishida, and Doug Sipp for their assistance. This investigation was financially supported by RIKEN.
　
References 
　
1. Obokata, H. et al. Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature 505, 641–647 (2014); retraction 511, 112 (2014). 
2. Obokata, H. et al. Bidirectional developmental potential in reprogrammed cells with acquired pluripotency. Nature 505, 676–680 (2014); retraction 511, 112 (2014).
3. Ying, Q. L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519–523 (2008). 
4. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows– Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
5. Robinson, J. T. et al. Integrative genomics viewer. Nature Biotechnol. 29, 24–26 (2011). 
6. Zeitouni, B. et al. SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics 26, 1895–1896 (2010).

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