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Sample GSM4039044 Query DataSets for GSM4039044
Status Public on Nov 27, 2020
Title FTW-eqiPSC.r2.H3K4me3
Sample type SRA
 
Source name Embryonic cells
Organism Equus ferus
Characteristics cell type: FTW-induced pluripotent stem cell
antibody: H3K4me3
Growth protocol C57BL/6 female mice (8–10 weeks old) were superovulated by intraperitoneal (IP) injection with 5 IU of PMSG (Prospec, Israel), followed by IP injection with 5 IU of hCG 48 h later. After mated with C57BL/6 male mice, embryos at 8-cell to morula stages were harvested at E2.75 (day of virginal plug = E0.5) in KSOM-Hepes (Wu et al., 2017) by flushing oviducts and uterine. They were cultured in the mKSOMaa (Wu et al., 2017) for overnight to form blastocysts until mESC injection in a humidified atmosphere containing 5% (v/v) CO2 and 5% (v/v) O2 at 37 °C. CD-1 females (8 weeks old or older) in natural estrous cycles were mated with CD-1 males. Blastocysts were harvested at E3.5 by flushing uterine horns, and cultured until Eq-iPSC injection.Vitrified equine embryos were thawed in a series of pre-warmed solutions: 0.25, 0.15, and 0 M sucrose in Hanks buffer (Gibco) containing 20% FBS. After thawing, embryos were cultured on the MEF in FTW medium overnight until blastocysts formed in a humidified atmosphere containing 5% (v/v) CO2 and 20% (v/v) O2 at 37 °C.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with an antibody.
ChIP-Seq libraries were prepared from size-selected ChIP DNA according to the standard Illimina library preparation protocol
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Equine FTW-induced pluripotent stem cell, repeat2, H3K4me3 (ChIP-seq)
Data processing We examined the global deposition of histone 3 lysine 4 trimethylation (H3K4me3) and histone 3 lysine 27 trimethylation (H3K27me3) in FTW-ESCs using ChIP-sequencing (ChIP-seq) 22.
Our analysis revealed that H3K4me3 levels were similar between FTW-ESCs and naïve ESCs, which were higher than primed EpiSCs.
Interestingly, a pronounced reduction of H3K27me3 deposition was observed in FTW-ESCs (Fig 1j).
These results indicate that FTW-ESCs are distinct from mouse ESCs and EpiSCs at both transcriptome and epigenome levels, and presumably exist in an intermediate pluripotent state between naïve and primed.
Genome_build: EquCab3.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: bigWig file for each sample.
 
Submission date Aug 19, 2019
Last update date Nov 28, 2020
Contact name CNSA CNGB
Organization name BGI
Street address BGI
City shenzhen
ZIP/Postal code 518083
Country China
 
Platform ID GPL27111
Series (2)
GSE135990 Derivation of formative-like pluripotent stem cells from mammalian embryos [ChIP-Seq]
GSE135991 Derivation of formative-like pluripotent stem cells from mammalian embryos
Relations
BioSample SAMN12601485
SRA SRX6742779

Supplementary file Size Download File type/resource
GSM4039044_Eq-iPSCs-Repeat-2-JW6_S6_R1_001.bw 8.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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