Expression data from ESC and in vitro derived somatic cells and germ cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: John Vincent
PROVIDER: E-GEOD-33121 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:In mammals, sex differentiation of primordial germ cells (PGCs) is determined by extrinsic cues from the environment1. In female PGCs, expression of Stimulated by retinoic acid 8 (Stra8) and meiosis are induced in response to retinoic acid (RA) provided by the mesonephroi2-4. Given the widespread role of RA signaling during development8,9, the molecular mechanism specifying the competence of PGCs to timely express Stra8 and enter meiosis are unknown2,10. Here we identify gene dosage dependent roles in PGC development for Ring1 and Rnf2, two central components of the Polycomb Repressive Complex 1 (PRC1)11,13. Both paralogs are essential for PGC development between day 10.5 and 11.5 of gestation. Rnf2 is subsequently required in female PGCs for maintaining high levels of Oct4 and Nanog expression6, and for preventing premature induction of meiotic gene expression and entry into meiotic prophase. Chemical inhibition of RA signaling partially suppresses precocious Oct4 down-regulation and Stra8 activation in Rnf2-deficient female PGCs. Chromatin immunoprecipitation analyses show that Stra8 is a direct target of PRC1 and PRC2 in PGCs. These data demonstrate the importance of PRC1 gene dosage in PGC development and in coordinating the timing of sex differentiation of female PGCs by antagonizing extrinsic RA signaling. Gene expression of mouse primordial germ cells was analysed using RNAseq method. Primodial germ cells were purified from embryos carrying Oct4(-delta-PE)-GFP transgene by FACS.
2013-03-14 | E-GEOD-42852 | biostudies-arrayexpress
Project description:Transcriptomes of mouse E12.5 primordial germ cells (PGCs), primordial germ cell-like cells (PGCLCs) isolated from 6-day culture embryoid bodies, and the precursor pluripotent stem cells [embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs)] and epiblast-like cells (EpiLCs) Total RNA was isolated from FACS-enriched, SSEA1+/CD61+ double-positive PGCs and PGCLCs. RNA was also isolated from ESC, iPSC, and EpiLC cultured without enrichment. Transcriptomes were determined using Affymetrix microarray.
2016-08-22 | E-GEOD-80983 | biostudies-arrayexpress
Project description:We performed RNA-Seq analyses on 15 human fetal samples at 53-137 days of development, 9 female and 5 male, and identified the transcriptional changes during the transition of human cKIT+ primordial germ cells (PGCs), the precursors of gametes, to the generation of Advanced Germline Cells. Comparing the transcriptional profile of PGCs to that of H1 and UCLA1 hESCs identifies differences between the two cell types and pinpoints molecules that can be used in the development of in vitro germ cell differentiation protocols starting from human pluripotent stem cells. RNA-Seq of cKIT+ cells analyzed from 6 biological samples for testes and 9 samples for ovaries from 53-137 days. 2 biological replicates of TRA-1-81+ cells sorted from H1 and UCLA1 hESCs. WGBS of cKIT+ cells analyzed from 4 biological samples of ovaries and 1 biological sample of testes at 57-137 days of development.
2015-05-28 | E-GEOD-63392 | biostudies-arrayexpress
Project description:Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12. Global gene expression changes following Dazl knockdown in in vitro primordial germ cells. In vitro primordial germ cells carrying control and Dazl knockdown shRNAs were generated from Oct4-GFP ES cells and isolated by FACS analysis. The global gene expression profiles were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays.
2013-12-31 | E-GEOD-39535 | biostudies-arrayexpress
Project description:Pig embryonic stem cells (ESCs) have been considered as an important candidate for preclinical researches on human therapy. However, the lack of understanding of pig pluripotent networks has hampered establishment of authentic pig ESCs. Here, we report that FGF2, ACTVIN, and WNT signaling is essential for maintaining pig pluripotency in vitro. Pig ESC lines derived by stimulating three signlaings formed colonies of flattened monolayer morphology. Newly derived ESCs were stably maintained over an extended period, and were capable of forming teratomas comprising three germ layers. Immunostaining showed that the stem cells expressed pluripotency markers including OCT4, SOX2, NANOG, SSEA1, and SSEA4. Transcriptome analysis showed that pig ESCs were developmentally similar to late epiblasts of preimplantation embryos and in terms of biological functions resembled human rather than mouse ESCs. However, the pig ESCs had distinct features such as coexpression of SSEA1 and SSEA4, two active X chromosomes, and a unique transcriptional pattern. In conclusion, we successfully derived authentic pig ESCs using novel cell culture conditions. Our findings will facilitate both the development of large animal models for human stem cell therapy and the generation of pluripotent stem cells from other domestic animals for agricultural use.
2019-07-08 | GSE120031 | GEO
Project description:We performed gene expression profiling on in vitro derived PGCs, undifferentiated ESCs, and somatic cells from the EB to examine germ cell expression in ESC-derived cells
2011-12-15 | GSE33121 | GEO
Project description:Embryonic stem cells (ESCs) and primordial germ cells (PGCs) express many pluripotency-associated genes, but ESCs do not normally undergo conversion into PGCs. Thus, we predicted that there is a mechanism that represses PGC-related gene expression in ESCs. Here we identify genes involved in this putative mechanism, by using an ESC line with a Vasa reporter for an RNAi screen of transcription factor genes expressed in ESCs. We identify 5 genes that result in the expression of Vasa when silenced. Of these, Max is the most striking. Transcriptome analysis reveals that Max knockdown (KD) in ESCs results in selective, global derepression of germ-cell-specific genes. Max interacts with histone H3K9 methyltransferases and associates with the germ-cell-specific genes in ESCs. In addition, Max-KD results in a decrease in histone H3K9 dimethylation at their promoter regions. We propose that Max is part of a protein complex that acts as a repressor of germ-cell-related genes in ESCs. Gene expression profile of Vasa-positive cells isolated from Max knockdown ESCs was compared to that of normal ESCs and in vivo PGCs. As an ESCs sample, a mouse embryonic stem cell line that carries a Venus reporter driven by the Vasa gene promoter (VV3) was used for this study. VV3 ESCs were transfected with non-silencing negative control siRNA (AllStars) or siRNA against the Max gene. Vasa-positive cells were purified using fluorescence-activated cell sorting (FACS). As a PGCs sample, a mouse strain that carries a germ-cell-specific GFP reporter (Oct4M-NM-^TPE-GFP) was used. PGCs were also purified using FACS. RNA samples were isolated from each sample and labeled and hybridized to Agilent microarrays. Three biological replicates were performed for each group of samples.
2013-05-01 | E-GEOD-45181 | biostudies-arrayexpress
Project description:Zebrafish Primordial Germ Cells (PGCs) were tracked in the Tg(Buc-GFP) line where the germ plasm protein Buc is fused to GFP. GFP-positive cells were isolated via FACS and RNA-seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256-cell, high, dome, 10 somites and prim-5 stages. Two hundred cells were used for each biological replicate.
2020-12-24 | E-MTAB-8741 | biostudies-arrayexpress
Project description:Embryonic stem cells (ESCs) comprise at least two populations of cells with divergent states of pluripotency. Here, we show that epiblast stem cells (EpiSCs) also comprise two distinct cell populations that can be distinguished by the expression of a specific Oct4-GFP marker. These two subpopulations, Oct4-GFP positive and negative EpiSCs, are capable of converting into each other in vitro. Oct4-GFP positive and negative EpiSCs are distinct from ESCs with respect to global gene expression pattern, epigenetic profile, and Oct4 enhancer utilization. Oct4-GFP negative cells share features with cells of the late mouse epiblast and cannot form chimeras. However, Oct4-GFP positive EpiSCs, which only represent a minor EpiSC fraction, resemble cells of the early epiblast and can readily contribute to chimeras. Our findings suggest that the rare ability of EpiSCs to contribute to chimeras is due to the presence of the minor EpiSC fraction representing the early epiblast.
2011-02-24 | GSE17984 | GEO
Project description:Derivation and maintenance of pluripotent stem cells (PSCs) including embryonic stem cells(ESCs) and (iPSCs) usually requires optimization of complex culture media, which hinders the generation of PSCs from various species. Expression of Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into iPSCs, even for species possessing no optimal culture condition. Here we explored whether expression of OSKM could induce and maintain pluripotency without specific growth factors and signaling inhibitors. Tet-On-OSKM/Oct4-GFP Mouse ESCs (mESCs) were derived from the embryos obtained after mating of Tet-On-OSKM mouse and Oct4-GFP mouse under the 2iL ( N2B27 plus MEK inhibitor PD0325901, GSK3β inhibitor ChIR99021, and leukemia inhibitory factor) condition. Tet-On-OSKM mouse was Gt(ROSA)26Sor tm1(rtTA*M2)Jae Col1a1 tm3(tetO-Pou5f1,-Sox2,-Klf4,-Myc)Jae/J(The Jackson Laboratory,011004), and Oct4-GFP mouse was B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J (The Jackson Laboratory,004654).The culture medium of Tet-On-OSKM/Oct4-GFP mouse ESCs was switched from 2iL to N2B27 plus Doxycycline medium (OSKM medium), under which OSKM trangene was activated. These above cells switched from 2iL to OSKM medium were called OSKM-ESCs. Meanwhile 2iL-ESCs (continuely cultured in 2iL) served as the positive control group. 2iL-ESCs and OSKM-ESCs collected at selective days (d18, 25 and 38) after medium switch were collected for RNA-Seq. Moreover, Tet-On-OSKM mouse embryonic fibroblast (MEF) cells were reprogrammed under OSKM medium (N2B27 plus Doxycycline) and 2iL medium, respectively. The resulting OSKM-iPSCs were reprogrammed and cultured under OSKM medium.The 2iL-iPSCs were reprogrammed under 2iL plus Doxycycline medium and cultured under 2iL medium (without Doxycycline)once clones were picked up.RNA-Seq of these above samples was conducted to analyze gene expression. We found that via continuous expression of OSKM,OSKM-ESCs and OSKM-iPSCs propagated stably, expressed pluripotency marker genes, and formed three germ layers in teratomas. Importantly, OSKM-iPSCs could produce gene-modified animals through germline transmission.Transcriptional landscapes of OSKM-iPSCs resembled 2iL-ESCs, and were more similar to those of ESCs cultured in serum/LIF.
2021-08-24 | GSE173471 | GEO