Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA312531 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3178170.fastq.gz | Fastqsanger.gz | |||
| SRR3178171.fastq.gz | Fastqsanger.gz | |||
| SRR3178162.fastq.gz | Fastqsanger.gz | |||
| SRR3178172.fastq.gz | Fastqsanger.gz | |||
| SRR3178163.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We mapped the genome-wide occupancy of Oct4 at G2/M (nocodazole-treated cells) and G1 phase (release of nocodazole-treated cells) in E14 mouse embryonic stem cells.
2016-04-19 | GSE78073 | GEO
Project description:Cell cycle and differentiation decisions are tightly linked; however, the underlying principles that drive these decisions are not fully understood. Here, we combined cell-cycle reporter system and single-cell RNA-seq profiling, to study the transcriptomes of mouse embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying a retinoic acid-based differentiation protocol we show that only cells in the G2/M phase are capable of differentiating into extraembryonic endoderm cells (XENs), whereas cells in the G1 phase predominantly produce epiblast stem cells (EpiSCs). Mechanistically, we show that Esrrb is a potent XEN state inducer as it is predominantly upregulated during G2/M phase, and cells engineered to overexpress Esrrb during G1 phase forced the cells to become XENs. Interestingly, this phenomenon is unique to the pluripotency ground state as sorting cells after 48 hours of differentiation resulted in a cell cycle-independent differentiation decisions. Cells in both G1 and G2/M phases contributed equally to EpiSC and XEN cellular lineages. Taken together, this study reveals an important functional link between cell-cycle states of pluripotent cells and lineage decisions, emphasizing the regulatory role of cell cycle during exit from pluripotency and can be further expand our understanding of early differentiation events.
2022-05-19 | GSE178390 | GEO
Project description:DNA methylomes at base resolution of mouse embryonic fibroblasts in G1 and G2 phase of cell cycle
| PRJNA358740 | ENA
Project description:Chavez2009 - a core regulatory network of OCT4 in human embryonic stem cells
A core OCT4-regulated network has been identified as a test case, to analyase stem cell characteristics and cellular differentiation.
This model is described in the article:
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach.
Chavez L, Bais AS, Vingron M, Lehrach H, Adjaye J, Herwig R
BMC Genomics, 2009, 10:314
Abstract:
BACKGROUND: The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self renewal are controlled by a transcription regulatory network governed by the transcription factors OCT4, SOX2 and NANOG. Recent studies on reprogramming somatic cells to induced pluripotent stem cells highlight OCT4 as a key regulator of pluripotency.
RESULTS: We have carried out an integrated analysis of high-throughput data (ChIP-on-chip and RNAi experiments along with promoter sequence analysis of putative target genes) and identified a core OCT4 regulatory network in human embryonic stem cells consisting of 33 target genes. Enrichment analysis with these target genes revealed that this integrative analysis increases the functional information content by factors of 1.3 - 4.7 compared to the individual studies. In order to identify potential regulatory co-factors of OCT4, we performed a de novo motif analysis. In addition to known validated OCT4 motifs we obtained binding sites similar to motifs recognized by further regulators of pluripotency and development; e.g. the heterodimer of the transcription factors C-MYC and MAX, a prerequisite for C-MYC transcriptional activity that leads to cell growth and proliferation.
CONCLUSION: Our analysis shows how heterogeneous functional information can be integrated in order to reconstruct gene regulatory networks. As a test case we identified a core OCT4-regulated network that is important for the analysis of stem cell characteristics and cellular differentiation. Functional information is largely enriched using different experimental results. The de novo motif discovery identified well-known regulators closely connected to the OCT4 network as well as potential new regulators of pluripotency and differentiation. These results provide the basis for further targeted functional studies.
This model is hosted on BioModels Database
and identified
by: MODEL1305010000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2005-01-01 | MODEL1305010000 | BioModels
Project description:Chickarmane2006 - Stem cell switch reversible
Kinetic modeling approach of the transcriptional dynamics of the embryonic stem cell switch.
This model is described in the article:
Transcriptional dynamics of the embryonic stem cell switch.
Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C
PLoS Computational Biology. 2006; 2(9):e123
Abstract:
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the transcription factors OCT4, SOX2, and NANOG. In addition to regulating each other through feedback loops, these genes also regulate downstream target genes involved in the maintenance and differentiation of embryonic stem cells. A search for the OCT4-SOX2-NANOG network motif in other species reveals that it is unique to mammals. With a kinetic modeling approach, we ascribe function to the observed OCT4-SOX2-NANOG network by making plausible assumptions about the interactions between the transcription factors at the gene promoter binding sites and RNA polymerase (RNAP), at each of the three genes as well as at the target genes. We identify a bistable switch in the network, which arises due to several positive feedback loops, and is switched on/off by input environmental signals. The switch stabilizes the expression levels of the three genes, and through their regulatory roles on the downstream target genes, leads to a binary decision: when OCT4, SOX2, and NANOG are expressed and the switch is on, the self-renewal genes are on and the differentiation genes are off. The opposite holds when the switch is off. The model is extremely robust to parameter changes. In addition to providing a self-consistent picture of the transcriptional circuit, the model generates several predictions. Increasing the binding strength of NANOG to OCT4 and SOX2, or increasing its basal transcriptional rate, leads to an irreversible bistable switch: the switch remains on even when the activating signal is removed. Hence, the stem cell can be manipulated to be self-renewing without the requirement of input signals. We also suggest tests that could discriminate between a variety of feedforward regulation architectures of the target genes by OCT4, SOX2, and NANOG.
This model is hosted on BioModels Database
and identified by: MODEL7957907314
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
2024-09-02 | BIOMD0000000203 | BioModels
Project description:Chickarmane2006 - Stem cell switch irreversible
Kinetic modeling approach of the transcriptional dynamics of the embryonic stem cell switch.
This model is described in the article:
Transcriptional dynamics of the embryonic stem cell switch.
Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C
PLoS Computational Biology. 2006; 2(9):e123
Abstract:
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the transcription factors OCT4, SOX2, and NANOG. In addition to regulating each other through feedback loops, these genes also regulate downstream target genes involved in the maintenance and differentiation of embryonic stem cells. A search for the OCT4-SOX2-NANOG network motif in other species reveals that it is unique to mammals. With a kinetic modeling approach, we ascribe function to the observed OCT4-SOX2-NANOG network by making plausible assumptions about the interactions between the transcription factors at the gene promoter binding sites and RNA polymerase (RNAP), at each of the three genes as well as at the target genes. We identify a bistable switch in the network, which arises due to several positive feedback loops, and is switched on/off by input environmental signals. The switch stabilizes the expression levels of the three genes, and through their regulatory roles on the downstream target genes, leads to a binary decision: when OCT4, SOX2, and NANOG are expressed and the switch is on, the self-renewal genes are on and the differentiation genes are off. The opposite holds when the switch is off. The model is extremely robust to parameter changes. In addition to providing a self-consistent picture of the transcriptional circuit, the model generates several predictions. Increasing the binding strength of NANOG to OCT4 and SOX2, or increasing its basal transcriptional rate, leads to an irreversible bistable switch: the switch remains on even when the activating signal is removed. Hence, the stem cell can be manipulated to be self-renewing without the requirement of input signals. We also suggest tests that could discriminate between a variety of feedforward regulation architectures of the target genes by OCT4, SOX2, and NANOG.
This model is hosted on BioModels Database
and identified by: MODEL7957942740
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
2024-09-02 | BIOMD0000000204 | BioModels
Project description:Dramatic change in DNA methylation patterns and levels both globally and/or locus-specifically is associated with the process of cell lineage specification and somatic reprogramming. We found the expression of DNA methyltransferase 1 (Dnmt1), the enzyme that maintains 5-methylcytosine (5mC) after DNA replication, is tightly regulated by the progression of cell cycle. Upregulation of Dnmt1 was observed in cells with shortened G1 and G2 phase. We hypothesize that 5mC level is not completely recovered by Dnmt1 immediately after DNA replication. In the attempt to clarify DNA methylation status before and after DNA replication, we performed Whole Genome Bisulfite Sequencing (WGBS) to map genome-wide DNA methylation separately in G1 and G2 phase of mouse embryonic fibroblasts (MEFs). Cells of different cell cycle phases were sorted by flow cytometry after Propidium iodide (PI) staining. We find an average of 2% decrease of global DNA methylation in G2 phase compared with G1, with the trend more magnificent in high CpG density regions. Generally, the results indicate that the G1 phase of cell cycle is an important time window for the stability of DNA methylation inheritance.
2017-10-13 | GSE92903 | GEO
Project description:DNA methylation is an essential for genome stability and mammalian embryonic development. DNA methyltransferase 1 (DNMT1) maintains cellular DNA methylation profile and its loss causes embryonic lethality. In this study, immunofluorescence staining, which can compare the difference between sister chromatids, were performed in mouse embryonic stem cells (ESCs) and suggest that the timing and region of de novo methylation by DNMT3 are restricted in DNMT1-deficient ESCs. To reanalyze the timing of de novo methylation by DNMT3, we collected cells from G1 to early S phases (called G1), cells in the mid-S phase, and cells in late S, G2, and M phases (called G2) by FACS, respectively. Among them, two cell populations, G1 and G2, were used for Me/hMeDIP-seq. As a result, the 5mC and 5hmC were globally decreased in the G2 cells.
2022-03-20 | GSE179515 | GEO
Project description:Human embryonic stem cells (hESCs) exhibit unique cell cycle structure, self-renewal and pluripotency. The Forkhead box transcription factor M1 (FOXM1) is critically required for the maintenance of pluripotency in mouse embryonic stem cells and mouse embryonal carcinoma cells, but its role in hESCs remains unclear. Here, we show that FOXM1 expression was enriched in undifferentiated hESCs and was regulated in a cell cycle-dependent manner with peak levels detected at the G2/M phase. Expression of FOXM1 did not correlate with OCT4 and NANOG during in vitro differentiation of hESCs. Importantly, knockdown of FOXM1 expression led to aberrant cell cycle distribution with impairment in mitotic progression but showed no profound effect on the undifferentiated state. Interestingly, FOXM1 depletion sensitized hESCs to oxidative stress. Moreover, genome-wide analysis of FOXM1 targets by ChIP-seq identified genes important for M phase including CCNB1 and CDK1, which were subsequently confirmed by ChIP and RNA interference analyses. Further peak set comparison against a differentiating hESC line and a cancer cell line revealed substantial difference in the genomic binding profile of FOXM1 in hESCs. Taken together, our findings provide the first evidence to support FOXM1 as important regulator of cell cycle progression and defense against oxidative stress in hESCs.
2016-04-08 | GSE79694 | GEO
Project description:The experiment was designed to look into transcriptional changes during cell cycle progression in human embryonic stem cells (hESCs). For this, FUCCI hESCs are sorted in Early G1 (EG1), Late G1 (LG1), and S/G2/M phases in triplicates, RNA was extracted and PolyA purified libraries were generated and sequenced in one HIGH Output NextSeq run Cycle, 2 X 75bp, paired-end reads.
2023-06-24 | E-MTAB-8347 | biostudies-arrayexpress