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| Status |
Public on Nov 27, 2020 |
| Title |
FTW-eqiPSC.r2.H3K4me3 |
| Sample type |
SRA |
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| Source name |
Embryonic cells
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| Organism |
Equus ferus |
| Characteristics |
cell type: FTW-induced pluripotent stem cell
antibody: H3K4me3
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| 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.
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Equine FTW-induced pluripotent stem cell, repeat2, H3K4me3 (ChIP-seq)
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| 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.
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| Submission date |
Aug 19, 2019 |
| Last update date |
Nov 28, 2020 |
| Contact name |
CNSA CNGB |
| Organization name |
BGI
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| Street address |
BGI
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| City |
shenzhen |
| ZIP/Postal code |
518083 |
| Country |
China |
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| 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 |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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