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| Status |
Public on Aug 14, 2018 |
| Title |
Mammalian embryo comparison identifies novel pluripotency genes associated with the naïve or primed state |
| Organisms |
Sus scrofa; Bos taurus; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
During early mammalian development transient pools of pluripotent cells emerge that can be immortalised upon stem cell derivation. The pluripotent state, "naïve" or "primed", depends on the embryonic stage and derivation conditions used. Here we analyse the temporal gene expression patterns of mouse, cattle and porcine embryos at stages that harbour different types of pluripotent cells. We document conserved and divergent traits in gene expression, and identify predictor genes shared across the species that are associated with pluripotent states in vivo and in vitro Amongst these are the pluripotency-linked genes Klf4 and Lin28b The novel genes discovered include naïve- (Spic, Scpep1 and Gjb5) and primed-associated (Sema6a and Jakmip2) genes as well as naïve-to primed transition genes (Dusp6 and Trip6). Both Gjb5 and Dusp6 play a role in pluripotency since their knockdown results in differentiation and downregulation of key pluripotency genes. Together, our interspecies comparison revealed new insights of pluripotency, pluripotent stem cell identity and a new molecular criterion for distinguishing between pluripotent states in various species including human.
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| Overall design |
RNA-Seq profiles of three embryonic stages, 3 replicas per stage. This profiling is performed for mouse (mus musculus), pig (sus scrofa) and cow (bos taurus). Furthermore 4 RNA-Seq samples on mouse liver RNA to investigate various methods of amplification for small quantities of RNA.
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| Contributor(s) |
Marks H, Bernardo AS, Jouneau A, Kensche P, Freude K, Tan Y, Kobolak J, Feher A, Polgar Z, Sartori C, Bock I, Louet C, Faial T, Hall V, Maseyakhi K, Huynen M, Lazzari G, Hyttel P, Stunnenberg H, Pedersen R, Dinnyes A |
| Citation(s) |
30026265, 30767785 |
| Submission date |
Dec 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hendrik Marks |
| E-mail(s) |
h.marks@ncmls.ru.nl
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| Organization name |
Radboud University Nijmegen, RIMLS
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| Department |
Molecular Biology
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| Street address |
Geert Grooteplein 26/28
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| City |
Nijmegen |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
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| Platforms (4)
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| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL11429 |
Illumina HiSeq 2000 (Sus scrofa) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL15749 |
Illumina HiSeq 2000 (Bos taurus) |
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| Samples (34)
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| Relations |
| BioProject |
PRJNA231898 |
| SRA |
SRP034545 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53387_RAW.tar |
4.1 Gb |
(http)(custom) |
TAR (of BEDGRAPH, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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