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Series GSE84164 Query DataSets for GSE84164
Status Public on Jul 27, 2017
Title Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Inhibitors of MEK1/2 and Gsk3b, known as '2i' culture conditions, enhance the derivation of embryonic stem cells (ESCs) and promote ground-state pluripotency in rodents 1,2. Here we show that the derivation of female mouse ESCs in the presence of 2i (2i-ESCs) results in a widespread loss of DNA methylation including a massive erasure of genomic imprints. Despite this global loss of DNA methylation, the early-passage 2i-ESCs efficiently differentiate into somatic cells and this process requires genome-wide de novo DNA methylation. However, the majority of imprinting control regions (ICRs) remain unmethylated in the 2i-ESC-derived differentiated cells. Consistently, 2i-ESCs exhibit impairment of autonomous embryonic and placental development by tetraploid embryo complementation and nuclear transplantation. We identified the derivation conditions of female ESCs that display 2i-ESC-like transcriptional signatures while preserving gamete-derived DNA methylation and autonomous developmental potential. Upon prolonged culture, however, female ESCs exhibit ICR demethylation, regardless of culture conditions. Our results provide insights into derivation of female ESCs reminiscent of ICM of preimplantation embryos.

S-ESCs are ESCs established under serum-containing medium. 2i_S_ESCs are ESCs established in 2i-containing medium, followed by maintenance in serum-containing medium.
Overall design Analyzing DNA methylation profiles and transcriptional profiles in 2i-ESCs, 2i-S-ESCs, 2i-MEFs, S-ESCs, t2i-ESCs, a2i-ESCs and MEFs for molecular analysis and 2n/4n injection and nuclear transfer for developmental assay for ESCs.
Contributor(s) Yamamoto T, Yamada Y
Citation(s) 28746308, 31056481
Submission date Jul 07, 2016
Last update date Jun 18, 2019
Contact name Yasuhiro Yamada
Organization name University of Tokyo
Department Institute of Medical Science
Lab Division of Stem Cell Pathology
Street address 4-6-1, Shirokanedai, Minato-ku
City Tokyo
ZIP/Postal code 108-8639
Country Japan
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (88)
GSM2228418 2i_ESC_15_female_methylseq
GSM2228419 2i_ESC_2_female_methylseq
GSM2228420 2i_ESC_23_male_methylseq
This SubSeries is part of SuperSeries:
GSE84165 Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation
BioProject PRJNA328171
SRA SRP078072

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
GSE84164_ProcessedDataMatrixRPKMfin.txt.gz 2.0 Mb (ftp)(http) TXT
GSE84164_RAW.tar 2.6 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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