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| Status |
Public on Aug 16, 2016 |
| Title |
Molecular Criteria for Defining the Naive Human Pluripotent State [methylation profiling] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Naive human pluripotent cells have been isolated in culture, but it remains unclear to what extent they resemble pluripotent cells in vivo. Here we present three lines of evidence indicating that naive pluripotent stem cells generated by small molecules share defining molecular signatures with the human preimplantation embryo. First, a comprehensive analysis of the transposcriptome reveals that naive human cells display a unique transposon expression profile of cleavage stage embryos. Second, induction of naive pluripotency is accompanied by a genome-wide depletion in DNA methylation that is reversible upon differentiation except at imprinted regions. Third, allele-specific analysis demonstrates that female naive cells exhibit an X chromosome signature of the human preimplantation embryo. However, when introduced into mouse embryos the naive cells failed to efficiently generate interspecies chimeras. Our work provides a set of molecular benchmarks for evaluating the developmental identity of distinct human pluripotent states captured in vitro.
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| Overall design |
Examine the methylomes of 6 naïve, 2 primed and 2 re-primed human embryonic stem cells
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| Contributor(s) |
Theunissen TW, Friedli M, He Y, Planet E, Oneil R, Markoulaki S, Wang H, Pontis J, Iouranova A, Imbeault M, Duc J, Cohen M, Wert KJ, Castanon RG, Zhang Z, Maetzel D, Huang Y, Nery JR, Drotar J, Lungjangwa T, Trono D, Ecker JR, Jaenisch R |
| Citation(s) |
27424783 |
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| Submission date |
Aug 16, 2016 |
| Last update date |
Aug 31, 2021 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
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| Phone |
8584534100
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| Organization name |
HHMI-Salk-Institute
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| Department |
Genomic Analysis Laboratory
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| Lab |
Ecker lab
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| Street address |
10010 North Torrey Pines Road
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE75868 |
Molecular Criteria for Defining the Naive Human Pluripotent State |
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| Relations |
| BioProject |
PRJNA339143 |
| SRA |
SRP085035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE85708_RAW.tar |
56.1 Gb |
(http)(custom) |
TAR (of TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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