KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, peptides, and recombinant proteins | ||
| Human FGF-basic recombinant protein | Thermo Fisher | PHG0023 |
| Critical commercial assays | ||
| Infinium methylation EPIC BeadChip kit | Illumina | WG-317-1001 |
| EZ DNA methylation kit | Zymo Research | D5001 |
| PureLink RNA mini kit | Invitrogen | 12183025 |
| Deposited data | ||
| GEO methylEPIC, RNA-seq, ATAC data series (GSE) | Banovich et al., 2018 | GSE89895 |
| GEO methy450K data series (GSE) | Butcher et al., 2016 | GSE59091 |
| GEO methyl450K data series (GSE) | Garitaonandia et al., 2015 | GSE34982 |
| GEO methyl450K data series (GSE) | Nazor et al., 2012 | GSE31848 |
| GEO methyl450K data series (GSE) | Nishizawa et al., 2016 | GSE60924 |
| GEO methyl450K data series (GSE) | Salomonis et al., 2016 | GSE85828 |
| GEO methyl450K data series (GSE) | Takasawa et al., 2018 | GSE73938 |
| GEO methyl450K data series (GSE) | Zdravkovic et al., 2015 | GSE72923 |
| GEO methylEPIC data series (GSE) for C19 and C23 passage experiment | This study | GSE167883 |
| Experimental models: cell lines | ||
| skin fibroblasts | NIA Aging Cell Repository, Coriell Institute | AG05278 |
| Euploid female hiPSC clone C19 from AG05278 | This study | C19 |
| Euploid female hiPSC clone C23 from AG05278 | This study | C23 |
| Oligonucleotides | ||
| XIST_F: AGCAGTTTGCCCTACTAGCTC | This study | XIST_Fwd |
| XIST_R: TAGCTGTTTGCAGTCCTCAGG | This study | XIST_Rev |
| TBP_F: TCACTGTTTCTTGGCGTGTG | This study | TBP_Fwd |
| TBP_R: TGGCAAACCAGAAACCCTTG | This study | TBP_Rev |
| HPRT_F: ATGCCACAGATAATACACATCCCC | This study | HPRT_Fwd |
| HPRT_R: CTCTCCAGAATAGTTAGATGTAGG | This study | HPRT_Rev |
| Recombinant DNA | ||
| CytoTune-iPS 2.0 Sendai reprogramming kit | ThermoFisher Scientific | A16517 |
| Software and algorithms | ||
| minfi | Aryee et al., 2014 | https://bioconductor.org/packages/release/bioc/html/minfi.html |
| tidyverse | Wickham et al., 2019 | https://www.tidyverse.org/ |
| ggsci | https://nanx.me/ggsci/articles/ggsci.html | https://github.com/nanxstats/ggsci |
| limma | Ritchie et al., 2015 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| biomaRt | Durinck et al., 2005 | https://bioconductor.org/packages/release/bioc/html/biomaRt.html |
| clusterProfiler | Yu et al., 2012 | https://guangchuangyu.github.io/software/clusterProfiler/ |
| numpy | Harris et al., 2020 | https://numpy.org/ |
| pandas | McKinney, 2010 | https://pandas.pydata.org/ |
| sklearn | Pedregosa et al., 2011 | https://scikit-learn.org |