Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA178509 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR609722.fastq.gz | Fastqsanger.gz | |||
| SRR609723.fastq.gz | Fastqsanger.gz | |||
| SRR609724.fastq.gz | Fastqsanger.gz | |||
| SRR609725.fastq.gz | Fastqsanger.gz | |||
| SRR609726.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:Transcriptome profiling of wild type and Tet1-null primordial germ cells (PGC) by Bisulfite-seq
| PRJNA181955 | ENA
Project description:The molecular mechanisms underlying the commitment of cells to the germ cell lineage and the subsequent formation of germ cells during mammalian development remain poorly understood due to an inability to obtain sufficient amounts of cellular materials to conduct thorough in-vitro analyses. Although primordial germ cells (PGCs) have been generated and isolated from embryonic stem cells (ESCs) in vitro, concurrent expression of several cell surface receptors and transcription factors, at various levels, confounds the identification of these cells. To date, only a few genes that mark the onset of germ cell commitment to the epiblast, including tissue nonspecific alkaline phosphatase (TNAP), Blimp1, Stella, and Fragilis, have been used with some degree of success to detect PGC formation in in-vitro model systems. In light of the current literature, the generation of an unlimited supply of germ cells and gametes from pluripotent stem cells would greatly facilitate studies into reproductive development. To accomplish this, we would need to discover novel markers that are specifically expressed in germ cells. Here we identified four genes that are specifically expressed in male and female germ cells, both in vivo and in vitro, but are not expressed in somatic tissues or ESCs. Expression of these genes therefore allows us to distinguish committed germ cells from undifferentiated pluripotent cell populations, a prerequisite for the successful derivation of germ cells and gametes in vitro. For RNA isolation, PGCs were sorted by FACS, collected by centrifugation, lysed in RLT buffer (QIAGEN), and processed using RNeasy Micro kits with on-column DNase digestion as per the manufacturer's instructions. Integrity of RNA samples was quality-checked using a 2100 Bioanalyzer (Agilent). If possible, 300 ng of total RNA per sample was used as starting material for linear amplification (Illumina TotalPrep RNA amplification kit, Ambion), which involved synthesis of T7-linked double-stranded cDNA and 14 hrs of in-vitro transcription incorporating biotin-labeled nucleotides. Purified and labeled cRNA was then quality-checked on a 2100 Bioanalyser, and hybridized as biological or technical duplicates for 18 hrs onto MouseRef-8 v2 gene expression BeadChips (Illumina), following the manufacturer's instructions. After being washed, the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader and accompanying software. 44 samples were analyzed. ESCm: OG2 male Embryonic Stem Cell, +/+ Oct4-GFP ES cells, 1 biological rep 11.5: 11.5 embryonic day PGC (Primordial Germ Cell), 2 biological reps 12.5F: 12.5 embryonic day female PGC (Primordial Germ Cell), 2 biological reps 13.5F: 13.5 embryonic day female PGC (Primordial Germ Cell), 2 biological reps 14.5F: 14.5 embryonic day female PGC (Primordial Germ Cell), 2 biological reps 15.5F: 15.5 embryonic day female PGC (Primordial Germ Cell), 2 biological reps 16.5F: 16.5 embryonic day female PGC (Primordial Germ Cell), 2 biological reps 17.5F: 17.5 embryonic day female PGC (Primordial Germ Cell), 2 biological reps 18.5F: 18.5 embryonic day female PGC (Primordial Germ Cell), 2 biological reps 12.5M: 12.5 embryonic day male PGC (Primordial Germ Cell), 2 biological reps 13.5M: 13.5 embryonic day male PGC (Primordial Germ Cell), 2 biological reps 14.5M: 14.5 embryonic day male PGC (Primordial Germ Cell), 2 biological reps 15.5M: 15.5 embryonic day male PGC (Primordial Germ Cell), 2 biological reps 16.5M: 16.5 embryonic day male PGC (Primordial Germ Cell), 2 biological reps 17.5M: 17.5 embryonic day male PGC (Primordial Germ Cell), 2 biological reps 18.5M: 18.5 embryonic day male PGC (Primordial Germ Cell), 2 biological reps 8M: 8 day after birth male PGC (Primordial Germ Cell), 2 biological reps 10M: 10 day after birth male PGC (Primordial Germ Cell), 2 biological reps 12M: 12 day after birth male PGC (Primordial Germ Cell), 2 biological reps 14M: 14 day after birth male PGC (Primordial Germ Cell), 1 biological rep 16M: 16 day after birth male PGC (Primordial Germ Cell), 2 biological reps 18M: 18 day after birth male PGC (Primordial Germ Cell), 2 biological reps 20M: 20 day after birth male PGC (Primordial Germ Cell), 2 biological reps
2010-11-16 | E-GEOD-23322 | biostudies-arrayexpress
Project description:Expression data from single cells from mouse primordial germ cell lineage (E6.25-E8.25, wild type and Blimp1KO)
| PRJNA106911 | ENA
Project description:ATAC-seq profiling of Nfat5 KO and wild type macrophages derived from bone marrow (primary cells), treated or not with Lipopolysaccharide (LPS).
2021-06-09 | GSE111476 | GEO
Project description:Maintenance and maturation of primordial germ cells is controlled by complex genetic and epigenetic cascades, and disturbances in this network lead to either infertility or malignant aberration. Transcription factor Tcfap2c / TFAP2C has been described to be essential for primordial germ cell maintenance and to be upregulated in several human germ cell cancers. Using global gene expression profiling, we identified genes deregulated upon loss of Tcfap2c in primordial germ cell-like cells. We show that loss of Tcfap2c affects many aspects of the genetic network regulating germ cell biology, such as downregulation maturation markers and induction of markers indicative of somatic differentiation, cell cycle, epigenetic remodeling, and pluripotency associated genes. Chromatin-immunoprecipitation analyses demonstrated binding of Tcfap2c to regulatory regions of deregulated genes (Sfrp1, Dmrt1, Nanos3, c-Kit, Cdk6, Cdkn1a, Fgf4, Klf4, Dnmt3b and Dnmt3l) suggesting that these genes are direct transcriptional targets of Tcfap2c in primordial germ cells. Since Tcfap2c deficient primordial germ cell like cells display cancer related deregulations in epigenetic remodeling, cell cycle and pluripotency control, the Tcfap2c-knockout allele was bred onto 129S2/Sv genetic background. There, mice heterozygous for Tcfap2c develop germ cell cancer with high incidence. Precursor lesions can be observed as early as E16.5 in developing testes displaying persisting expression of pluripotency markers. We further demonstrate, that mice with a heterozygous deletion of the Tcfap2c target gene Nanos3 are also prone to develop teratoma. These data highlight Tcfap2c as a critical and dose-sensitive regulator of germ cell fate. 8 samples were analyzed. Ctrl ESC: Control mouse embryonic stem cells (ESCs), 2 biological rep KO ESC: Tcfap2c knock-out mouse embryonic stem cells (ESCs), 2 biological rep Ctrl PGC: Control mouse primordial germ cells (PGCs), 2 biological rep KO PGC: Tcfap2c knock-out mouse primordial germ cells (PGCs), 2 biological rep
2014-01-30 | E-GEOD-45941 | biostudies-arrayexpress
Project description:The requirement for primordial germ cells (PGCs) during sexual differentiation is variable among vertebrates. It has been shown that in zebrafish complete loss of PGCs in the embryos causes exclusive male development. Further, transplantation of a single PGC into a germline deficient zebrafish embryos generates male exclusively, suggesting PGC number might be important for the ovarian fate.To explore how PGC number might regulate sexual development in zebrafish, we experimentally manipulated its number by injecting dnd MO into embryos to generate fish containing a spectrum of PGC number. The experiment was designed to compare transcriptomes between the developing trunk regions of wild type and dnd morphants at different developmental stages.
2015-05-08 | GSE57046 | GEO
Project description:The requirement for primordial germ cells (PGCs) during sexual differentiation is variable among vertebrates. It has been shown that in zebrafish complete loss of PGCs in the embryos causes exclusive male development. Further, transplantation of a single PGC into a germline deficient zebrafish embryos generates male exclusively, suggesting PGC number might be important for the ovarian fate.To explore how PGC number might regulate sexual development in zebrafish, we experimentally manipulated its number by injecting dnd MO into embryos to generate fish containing a spectrum of PGC number. The experiment was designed to compare transcriptomes between the developing trunk regions of wild type and dnd morphants at different developmental stages. The dnd MO was microinjected into one cell stage embryos to generate zebrafish with a range of PGC numbers. Transcriptomes of developing trunk regions of wild type and dnd morphants at 14 dpf and 22 dpf were analyzed.
2015-05-08 | E-GEOD-57046 | biostudies-arrayexpress
Project description:The molecular mechanisms of human primordial germ cell (PGC) specification are poorly understood due to the inaccessibility of cell materials and the lack of an alternative in vitro model that enables tracking of the earliest stages of germ cell development. Here, we introduce a defined and efficient differentiation system for the induction of pre-migratory PGC-like cells from human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). By step-wise differentiation, we generated an OCT4+/ T+/BLIMP1+ cell population that transitioned into STELLA expressing PGC-like cells that exhibited a similar key gene expression as mouse PGCs as well as global epigenetic reprogramming. Even though, these PGC-like cells expressed PRDM14 at very low levels, they underwent activation of pluripotency/PGC genes, suppression of neural induction and suppression of de novo DNA methylation, events that are regulated by Prdm14 during mouse PGC specification. This study demonstrates that human PGC commitment shares many key features with mouse PGC specification, but harbors unique and so far unknown mechanisms that, point to a novel human transcriptional regulation. 7 samples were analyzed. ESC: Human Embryonic Stem Cells, 1 biological rep iPSC: Human induced Pluripotent Stem Cells, 1 biological rep d2: Human induced Pluripotent Stem Cells, 2 days differentiation treatment , 2 biological rep d4PGCLC: Human induced Pluripotent Stem Cells, 4 days differentiation treatment towards Primordial Germ Cells Like Cells, 1 biological rep d6PGCLC: Human induced Pluripotent Stem Cells, 6 days differentiation treatment towards Primordial Germ Cells Like Cells, 2 biological rep
2015-04-06 | E-GEOD-53498 | biostudies-arrayexpress
Project description:Primordial germ cells (PGCs), the embryonic precursors of eggs and sperm, are a unique model for identifying and studying regulatory mechanisms in singly migrating cells. From their time of specification to eventual colonization of the gonad, mouse PGCs traverse through and interact with many different cell types, including epithelial cells and mesenchymal tissues. Work in drosophila and zebrafish have identified many genes and signaling pathways involved in PGC migration, but little is known about this process in mammals. We have generated a point mutation in the Ror2 gene that we know disrupts primordial germ cell migration in the developing mouse embryo. We used microarray analysis to determine if this defect is mediated through genome-wide or pathway-specific transcriptional changes. We analyzed primordial germ cells (PGCs) from 4 wild-type (WT) and 4 Ror2Y324C/Y324C mutant embryos using Oct4-DPE-EGFP. PGCs were collected during their active migratory state at embryonic day 9.5 (somite range 20-25).
2014-08-08 | E-GEOD-60179 | biostudies-arrayexpress
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