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| Status |
Public on May 20, 2022 |
| Title |
Transcriptomic analysis of porcine PSCs (pLCDM and pPSC(KOFL)) and pLCDM_TSC induced from pLCDM |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To further understand the biological characteristics of porcine pluripotent stem cells (pLCDM) established under LCDM system, transcriptome analyses were performed. The data showed that the biological events related to placental development were found in pLCDMs, while pLCDMs expressed more biological events related to embryo development and organ development of each layer than TE. Transcriptomic analysis demonstrated that pLCDMs expressed higher levels of trophoblast lineage genes than pPSCs (KOFL). Furthermore, we successfully induced trophoblastic-like cells and pLCDM_TSCs with high expression of trophoblast lineage marker genes in vitro using a pure chemical medium. To comprehensively analyze the difference between pLCDM_TSCs and pLCDMs, low input RNA-seq was performed on the cell lines. A total of 3,594 DEGs were found, and 1,606 genes were significantly upregulated in pLCDM_TSCs, including BMP signaling pathway related genes BMPR1A, ID1, and trophoblast lineage marker genes ITGA1, ITGA6, FZD5, etc. It was worth noting that we found 509 highly expressed genes in hTSCs among the genes that were highly expressed in pLCDM_TSCs. Together, these results demonstrated the unique cellular potency of pLCDMs for trophoblast lineage.
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| Overall design |
mRNA profiles of porcine PSCs (pLCDM and pPSC(KOFL)) and pLCDM_TSC induced from pLCDM
pLCDM: The porcine pluripotent stem cells which established from LCDM [1] (consists of human LIF, GSK3 inhibitor CHIR99021, G protein coupled receptors (GPCRs) inhibitor (S) - (+) -dimethindene maleate and PARP1 inhibitor minocycline hydrochloride) condition using blastocysts.
pLCDM-TSC: The pLCDMs were cultured in human TSC conditions.These pLCDM-derived TSC-like cells were referred to as pLCDM-TSCs in this study.
pPSC(KOFL): The porcine pluripotent stem cells which established from KOFL [2] (A novel chemically defined serum and feeder free medium) condition using blastocysts.
The icm and te samples have been re-analyzed from samples included in GSE139512. These samples have also been included here for completeness.
REFERENCES
[1] Yang Y, Liu B, Xu J et al. Derivation of Pluripotent Stem Cells with In Vivo Embryonic and Extraembryonic Potency. Cell. 2017;169(2):243-257 e225.
[2] Zhang X, Xue B, Li Y et al. A novel chemically defined serum- and feeder-free medium for undifferentiated growth of porcine pluripotent stem cells. J Cell Physiol. 2019.
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| Contributor(s) |
Yu Z, Zhou S, Liu M, Chen L, Zhang X, Yang X, Cui H, Jiang C, lv Y, Yan T, Kong Q, Liu Z |
| Citation |
Zhuoran Yu, Sihan Zhou, Minli Liu, Lijun Chen, Xue Zhang, Xu Yang, Hongdi Cui, Chaoqian Jiang, Yanjiao Lv, Tingsheng Yan, Qingran Kong, Zhonghua Liu. Porcine pluripotent stem cells established from LCDM medium with characteristics differ from human and mouse extended pluripotent stem cells. Stem Cells. DOI: 10.1093/stmcls/sxac034
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| Submission date |
Feb 25, 2022 |
| Last update date |
May 26, 2022 |
| Contact name |
Lijun Chen |
| E-mail(s) |
17754119527@139.com
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| Phone |
17754119527
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| Organization name |
wenzhou medical university
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| Street address |
chashan
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| City |
wenzhou |
| State/province |
zhejiang |
| ZIP/Postal code |
325000 |
| Country |
China |
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| Platforms (1) |
| GPL11429 |
Illumina HiSeq 2000 (Sus scrofa) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA810421 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE197451_pLCDM_vs_ICM_Raw_gene_counts_FPKM_matrix.txt.gz |
551.8 Kb |
(ftp)(http) |
TXT |
| GSE197451_pLCDM_vs_TE_Raw_gene_counts_FPKM_matrix.txt.gz |
554.4 Kb |
(ftp)(http) |
TXT |
| GSE197451_pLCDM_vs_pLCDM-TSC_Raw_gene_counts_FPKM_matrix.txt.gz |
640.8 Kb |
(ftp)(http) |
TXT |
| GSE197451_pLCDM_vs_pPSC_KOFL_Raw_gene_counts_FPKM_matrix.txt.gz |
600.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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