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Series GSE75868 Query DataSets for GSE75868
Status Public on Jul 18, 2016
Title Molecular Criteria for Defining the Naive Human Pluripotent State
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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 Please refer to individual Series. This SuperSeries is composed of the SubSeries listed below.
 
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 Dec 10, 2015
Last update date Apr 30, 2024
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
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 (40)
GSM1969063 WIBR2_4i
GSM1969064 WIBR3_4i
GSM1969065 WIBR3_5i
This SuperSeries is composed of the following SubSeries:
GSE83765 RNA-seq of naive and primed ES cells
GSE84382 ChIP-seq of naive and primed ES cells
GSE85689 RNA-seq of naive and primed ES cells (NHSM)
Relations
BioProject PRJNA305609

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75868_RAW.tar 57.4 Gb (http)(custom) TAR (of PILEUP, TSV, TXT)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data provided as supplementary file

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