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Series GSE53387 Query DataSets for GSE53387
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
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.
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.
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
Organization name Radboud University Nijmegen, RIMLS
Department Molecular Biology
Street address Geert Grooteplein 26/28
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (4)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL11429 Illumina HiSeq 2000 (Sus scrofa)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (34)
GSM1290643 mEBI1 RNA-Seq
GSM1290644 mEBI2 RNA-Seq
GSM1290645 mEBI3 RNA-Seq
BioProject PRJNA231898
SRA SRP034545

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE53387_RAW.tar 4.1 Gb (http)(custom) TAR (of BEDGRAPH, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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