| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Sendai Virus pAb (Polyclonal Antibody) | MBL International | Cat#PD029, RRID: AB_10597564 |
| Goat anti-Rabbit IgG Secondary Antibody Cyanine5 | Thermo Fisher Scientific | Cat#A10523, RRID: AB_2534032 |
| Pacific Blue anti-human HLA-A,B,C Antibody | BioLegend | Cat#311418, RRID: AB_493669 |
| Human TROP-2 (TACSTD2) Alexa Fluor 488-conjugated Antibody | R&D systems | Cat#FAB650G, RRID: not available |
| PE Mouse Anti-Human CD249 (ENPEP) | BD Biosciences | Cat#564533, RRID: AB_2738838 |
| TIM-1 (HAVCR1) Antibody, anti-human, Biotin, RE-Afinity | Miltenyi Biotec | Cat#130-106-023, RRID: AB_2654152 |
| APC Streptavidin | BioLegend | Cat#405207, RRID: not available |
| Bacterial and virus strains | ||
| CytoTune-iPS 2.0 | ID Pharma, Japan | Cat# 69000-41 |
| CytoTune-iPS 2.0L | ID Pharma, Japan | Cat# 69020-81 |
| CytoTuneEX-iPS (containing SeV18 + KLF4/PmiR367T2/TSΔF) | ID Pharma, Japan | Cat# 69060-61 |
| SeV18 + KLF4/TS12ΔF | ID Pharma, Japan | This paper |
| SeV18 + KLF4/PmiR367T2/TS12ΔF | ID Pharma, Japan | This paper |
| Chemicals, peptides, and recombinant proteins | ||
| CHIR99021 | Sigma-Aldrich | Cat#SML1046 |
| PD0325901 | Sigma-Aldrich | Cat#PZ0162 |
| Gö6983 | Sigma-Aldrich | Cat#G1918 |
| Recombinant Human LIF | Peprotech | Cat#300-05 |
| Y-27632 (hydrochloride) | Wako | Cat#036-24023 |
| DMEM/Ham’s F-12 | Sigma-Aldrich | Cat#D6421 |
| NDiff227 | Takara Bio | Cat#Y40002 |
| Matrigel ESC qualified Matrix | Corning | Cat#CLS354277 |
| iMatrix-511 (Laminin-E8) | Nippi, Japan | Cat#892012 |
| Stem-Cellbanker | Takara Bio | Cat#CB045 |
| Cell Banker 1 | Takara Bio | Cat#CB011 |
| Bovine Albumin Fraction V (7.5% solution) | Gibco | Cat#15260037 |
| Dimethyl sulfoxide | Sigma-Aldrich | Cat#D2650 |
| Accutase | Innovative Cell Technologies | Cat#AT104 |
| A83-01 | Wako | Cat#039-24111 |
| JAK Inhibitor I | Sigma-Aldrich | Cat#420099 |
| Recombinant Human BMP-4 Protein | R&D systems | Cat#314-BP |
| 7-AAD Viability Staining Solution | BioLegend | Cat#420403 |
| StemFit AK02N | Takara Bio | Cat#AK02N |
| DMEM (4.5 g/L Glucose) with L-Gln, without Sodium Pyruvate, liquid | Nacalai Tesque | Cat#08459-64 |
| StemSpan ACF | STEMCELL Technologies | Cat#09860 |
| Recombinant Human SCF Protein | R&D systems | Cat#255-SC |
| Recombinant Human Thrombopoietin (NS0-expressed) Protein | R&D systems | Cat#288-TPN |
| Recombinant Human Flt-3 Ligand/FLT3L Protein | R&D systems | Cat#308-FK |
| Recombinant Human IL-6 Protein | R&D systems | Cat#206-IL |
| Recombinant Human IL-3 Protein | R&D systems | Cat#203-IL |
| 4%-Paraformaldehyde Phosphate Buffer Solution | Nacalai Tesque | Cat#09154-85 |
| Triton X-100 | Nacalai Tesque | Cat#35501-15 |
| Hydrochloric Acid | Wako | Cat#080-01066 |
| DMEM/F-12, GlutaMAX supplement | Gibco | 10565018 |
| 2-Mercaptoethanol | Gibco | 21985023 |
| MEM Non-Essential Amino Acids Solution (100X) | Gibco | 11140050 |
| Critical commercial assays | ||
| AllPrep DNA/RNA Mini Kit | QIAGEN | Cat#80284 |
| RNase-Free DNase Set | QIAGEN | Cat#79256 |
| NucleoSpin miRNA | MACHEREY-NAGEL | Cat#740971.50 |
| PrimeScript RT Master Mix | Takara Bio | Cat#RR036B |
| TaqMan Advanced miRNA Assays | Applied Biosystems | Cat#A25576 |
| Fast SYBR Green Master Mix | Applied Biosystems | Cat#4385612 |
| TaqMan Fast Advanced Master Mix | Applied Biosystems | Cat#4444557 |
| TaqMan hPSC Scorecard Kit, 384-well | Applied Biosystems | Cat#A15872 |
| TaqMan hPSC Scorecard Panel, Fast 96-well | Applied Biosystems | Cat#A15876 |
| TruSeq Stranded Total RNA Library Prep Gold | Illumina | Cat#20020599 |
| HiSeq PE Cluster Kit v4-cBot | Illumina | Cat#PE-401-4001 |
| HiSeq SBS Kit v4 | Illumina | Cat#FC-401-4003 |
| NovaSeq 6000 S1 Reagent Kit v1.5 | Illumina | Cat#20028318 |
| NextSeq 500/550 High Output Kit v2.5 | Illumina | Cat#FC-404-2005 |
| EZ DNA Methylation Kit | Zymo Research | Cat#D5001 |
| Infinium HumanMethylation450 BeadChip Kit | Illumina | Cat#WG-314-1003 |
| Infinium MethylationEPIC BeadChip Kit | Illumina | Cat#WG-317-1001 |
| Infinium OmniExpress24 v1.3 DNA Analysis Kit | Illumina | Cat#20024631 |
| Deposited data | ||
| RNA-seq, DNA methylation array and SNP genotyping array data | This paper | GEO: GSE179476 |
| Raw images and analyzed data | This paper | https://doi.org/10.5281/zenodo.7101941 |
| Systematic Identification of Defined Conditions for Induction and Maintenance of Naive Human Pluripotency | Theunissen et al. (2014) | GEO: GSE59435 |
| Molecular Criteria for Defining the Naive Human Pluripotent State | Theunissen et al. (2016) | GEO: GSE75868 |
| Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq | Yan et al. (2013) | GEO: GSE36552 |
| RNA sequencing of conventional and reset human pluripotent stem cells | Takashima et al. (2014) | ArrayExpress: E-MTAB-2857 |
| Experimental models: Cell lines | ||
| Human embryonic stem cell line: H9 (WA09) | WiCell Research Institute | hPSCreg ID: WAe009-A |
| Human induced pluripotent stem cell line: 201B7 | Kyoto University | hPSCreg ID: KUIFMSi004-C |
| Human dermal fibroblast: TIG113 | JCRB Cell Bank | ID: JCRB0539 |
| Human dermal fibroblast: TIG120 | JCRB Cell Bank | ID: JCRB0542 |
| Human peripheral blood mononuclear cells (ID:HHU20120815) | Cellular Technology Ltd. | CTL-UP1 |
| Human peripheral blood mononuclear cells (ID:HHU20140120) | Cellular Technology Ltd. | CTL-UP1 |
| CF1 mouse embryonic fibroblasts, irradiated | ThermoFisher Scientific | A34181 |
| Oligonucleotides | ||
| SEV (Mr04269880_mr) | ThermoFisher Scientific | Cat#4331182 |
| GAPDH (Hs02786624_g1) | ThermoFisher Scientific | Cat#4331182 |
| hsa-miR-367-3p (478066_mir) | ThermoFisher Scientific | Cat#A25576 |
| hsa-miR-423-3p (478327_mir) | ThermoFisher Scientific | Cat#A25576 |
| Primer: SOX2 to M in SeV-KOS Forward: CTGCCCCTCTCACACATGT Reverse: GGGCTCCACAGTACCGTTAT |
This paper | N/A |
| Primer: LMYC to L in SeV-LMYC Forward: GAAAAGACAGCTCCGATGCC Reverse: CCTGCCCATCCATGACCTAG |
This paper | N/A |
| Primer: HN to CMYC in SeV-CMYC Forward: CTCTCAGTCTCTTACGTCTCTCA Reverse: CCTCCTCGTCGCAGTAGAAA |
This paper | N/A |
| Primer: Leader to KLF4 in SeV-KLF4 Forward: TTCCAGACCCTTTGCTTTGC Reverse: GCGAACGTGGAGAAAGATGG |
This paper | N/A |
| Primer: GAPDH Forward: TGCACCACCAACTGCTTAGC Reverse: TCTTCTGGGTGGCAGTGATG |
This paper | N/A |
| Software and algorithms | ||
| Graphpad Prism 9 | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo software 10.6.1 | FlowJo, LCC | https://www.flowjo.com/ |
| bcl2fastq v2.17.1.14 | Illumina | https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html |
| long-rna-seq-pipeline v2.3.4. | ENCODE DCC | https://github.com/ENCODE-DCC/long-rna-seq-pipeline/releases/tag/v2.3.4 |
| STAR 2.5.1b | Dobin et al. (2013) | https://github.com/alexdobin/STAR |
| RSEM 1.2.23 | Li and Dewey (2011) | https://github.com/deweylab/RSEM/releases/tag/v1.2.23 |
| Subread 1.5.1 | Liao et al. (2014) | https://sourceforge.net/projects/subread/files/subread-1.5.1/ |
| GenomeStudio V2011.1 | Illumina | https://support.illumina.com/downloads/genomestudio_software_20111.html |
| R 3.6.3 | The R Foundation for Statistical Computing | http://www.R-project.org/ |
| Minfi | Aryee et al. (2014) | https://bioconductor.org/packages/release/bioc/html/minfi.html |
| GenomeStudio v2.0.4 | Illumina | https://support.illumina.com/downloads/genomestudio-2-0.html |
| PennCNV 1.0.3 | Wang et al. (2007) | https://www.openbioinformatics.org/penncnv/penncnv_installation.html |
| Mosaic Alteration Detection-MAD (1.0.1) | González et al. (2011) | https://github.com/isglobal-brge/MAD/ |
| GWAS tools (1.16.1) | Gogarten et al. (2012) | https://www.bioconductor.org/packages/release/bioc/html/GWASTools.html |
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