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Series GSE85708 Query DataSets for GSE85708
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
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.
Overall design Examine the methylomes of 6 naïve, 2 primed and 2 re-primed human embryonic stem cells
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
Submission date Aug 16, 2016
Last update date Aug 31, 2021
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1969063 WIBR2_4i
GSM1969064 WIBR3_4i
GSM1969065 WIBR3_5i
This SubSeries is part of SuperSeries:
GSE75868 Molecular Criteria for Defining the Naive Human Pluripotent State
BioProject PRJNA339143
SRA SRP085035

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Supplementary file Size Download File type/resource
GSE85708_RAW.tar 56.1 Gb (http)(custom) TAR (of TSV)
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Raw data are available in SRA

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