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| Status |
Public on Nov 27, 2020 |
| Title |
FTW-eqESC#2.r2.RNA-seq |
| Sample type |
SRA |
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| Source name |
Embryonic cells
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| Organism |
Equus ferus |
| Characteristics |
cell type: FTW-embryonic stem cell
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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 |
polyA RNA |
| Extraction protocol |
RNA extraction was performed using a RNeasy Mini Kit (QIAGEN) using DNase treatment (QIAGEN).
RNA was analyzed using a 2100 Bioanalyzer (Aglient Technologies, USA). (Transcripts per Kilobase Million)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Equine FTW-embryonic stem cell#2, repeat2, RNA-seq
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| Data processing |
We also examined global transcriptional profile of FTW-ESCs via RNA-sequencing (RNA-seq) and compared them with published mouse ESCs and EpiSCs datasets.
Principle component analysis (PCA) and unsupervised hierarchical clustering and correlation (UHC) analysis showed that FTW-ESCs clustered tightly as a group separated from both naïve ESCs and primed EpiSCs, indicating that FTW-ESCs acquired a distinct transcriptome profile (Fig. 1g and Extended Data Fig. 3a).
Analysis of pluripotency specific genes21 confirmed that FTW-ESCs exhibited a pluripotency profile different from ESCs and EpiSCs (Extended Data Fig. 3b).
Comparative analysis identified 79 genes uniquely expressed in FTW-PSCs using a 2-fold cut-off (p < 0.05) (Fig. 3h and Supplementary Table 1).
Gene ontology (GO) terms enriched in genes upregulated in FTW-ESCs were related to embryonic morphogenesis, cell fate commitment, formation of primary germ layers among others (Fig. 1i).
Genome_build: EquCab3.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each sample.
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| Submission date |
Aug 19, 2019 |
| Last update date |
Nov 27, 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) |
| GSE135989 |
Derivation of formative-like pluripotent stem cells from mammalian embryos [RNA-Seq] |
| GSE135991 |
Derivation of formative-like pluripotent stem cells from mammalian embryos |
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| Relations |
| BioSample |
SAMN12601464 |
| SRA |
SRX6742762 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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