Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA350170 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4444890_1.fastq.gz | Fastqsanger.gz | |||
| SRR4444890_2.fastq.gz | Fastqsanger.gz | |||
| SRR4444891_1.fastq.gz | Fastqsanger.gz | |||
| SRR4444891_2.fastq.gz | Fastqsanger.gz | |||
| SRR4444882_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 46 |
Similar Datasets
Project description:Integrative analysis of reprogramming human fibroblast cells to naïve pluripotency
| PRJNA350224 | ENA
Project description:Integrative analysis of reprogramming human fibroblast cells to naïve pluripotency [RNA-seq]
| PRJNA350223 | ENA
Project description:Integrative analysis of reprogramming human fibroblast cells to naïve pluripotency [RRBS]
| PRJNA350172 | 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:Derivation of human naïve cells in the ground state of pluripotency provides promising avenues for developmental studies and therapeutic manipulations. However, the molecular mechanisms involved in establishment and maintenance of human naïve pluripotency remain poorly understood. Using the human inducible reprogramming system together with 5iLAF naïve induction strategy, we performed integrative analysis across the timeline from human fibroblasts to naïve iPSCs, which reveals ordered expression waves of gene networks sharing signatures with embryonic development process from post-implantation to pre-implantation stages. We also observed a significant transient re-activation of transcripts with 8-cell-stage-like characteristics in late naïve reprogramming stages. Moreover, combined quantitative proteomics analysis with transcriptional dynamics during naïve pluripotency induction, we identified ALPPL2 as the specific surface marker for human naïve pluripotency. Altogether, our study deepens the understanding of molecular mechanisms of human naïve pluripotency.
2018-03-03 | GSE89060 | GEO
Project description:Derivation of human naïve cells in the ground state of pluripotency provides promising avenues for developmental studies and therapeutic manipulations. However, the molecular mechanisms involved in establishment and maintenance of human naïve pluripotency remain poorly understood. Using the human inducible reprogramming system together with 5iLAF naïve induction strategy, we performed integrative analysis across the timeline from human fibroblasts to naïve iPSCs, which reveals ordered expression waves of gene networks sharing signatures with embryonic development process from post-implantation to pre-implantation stages. We also observed a significant transient re-activation of transcripts with 8-cell-stage-like characteristics in late naïve reprogramming stages. Moreover, combined quantitative proteomics analysis with transcriptional dynamics during naïve pluripotency induction, we identified ALPPL2 as the specific surface marker for human naïve pluripotency. Altogether, our study deepens the understanding of molecular mechanisms of human naïve pluripotency.
2018-03-03 | GSE89058 | GEO
Project description:Derivation of human naïve cells in the ground state of pluripotency provides promising avenues for developmental studies and therapeutic manipulations. However, the molecular mechanisms involved in establishment and maintenance of human naïve pluripotency remain poorly understood. Using the human inducible reprogramming system together with 5iLAF naïve induction strategy, we performed integrative analysis across the timeline from human fibroblasts to naïve iPSCs, which reveals ordered expression waves of gene networks sharing signatures with embryonic development process from post-implantation to pre-implantation stages. We also observed a significant transient re-activation of transcripts with 8-cell-stage-like characteristics in late naïve reprogramming stages. Moreover, combined quantitative proteomics analysis with transcriptional dynamics during naïve pluripotency induction, we identified ALPPL2 as the specific surface marker for human naïve pluripotency. Altogether, our study deepens the understanding of molecular mechanisms of human naïve pluripotency.
2018-03-03 | GSE89056 | GEO
Project description:Defining how human pluripotent cell identity is controlled and in particular how naïve pluripotency is acquired during cell reprogramming is crucial for the future applications of pluripotent stem cells. However, the regulatory pathways of naïve cell reprogramming remain incompletely understood. Here, we used genome-wide CRISPR-Cas9 screening to identify novel regulators of primed to naïve pluripotent stem cell reprogramming, including genes that are essential for reprogramming and genes that normally impede reprogramming and whose targeted deletion led to enhanced reprogramming. Integrated analysis defined specific chromatin complexes and signalling pathways as critical regulators of naïve reprogramming, and were largely distinct from regulators of somatic cell reprogramming. Mechanistically, PRC1.3 and PRDM14 are jointly required to transcriptionally repress developmental and gene regulatory factors to ensure naïve cell reprogramming. Additionally, small molecule inhibitors of reprogramming impediments increased the efficiency of naïve cell reprogramming, and are of practical benefit that can improve on current reprogramming methods. Taken together, we have identified novel regulators controlling the establishment of naïve pluripotency in human cells, which will open up new ways to exploit the full potential of pluripotent stem cells. These results also provide new insights into mechanisms that destabilise and reconfigure cell identity during cell state transitions.
2022-04-06 | PXD023547 | Pride
Project description:In contrast to conventional human pluripotent stem cells (hPSC) that are related to post-implantation embryo stages, naïve hPSC exhibit features of pre-implantation epiblast. Naïve hPSC are established by resetting conventional hPSC, or are derived from dissociated embryo inner cell masses. Here we investigate conditions for transgene-free reprogramming of human somatic cells to naïve pluripotency. We find that RNA-mediated induction of naïve pluripotency is enhanced by Wnt inhibition. We demonstrate application to independent human fibroblast cultures and endothelial progenitor cells and show that induced naïve hPSC can be clonally expanded with a diploid karyotype. They exhibit distinctive surface marker, transcriptome, and methylome properties of naïve epiblast identity. Induced naïve hPSC lines undergo somatic lineage differentiation following formative transition. Efficient, facile, and reliable induction of transgene free naïve hPSC offers a robust platform for delineation of human reprogramming trajectories and for evaluating the attributes of isogenic naïve versus conventional hPSC.
2019-12-02 | GSE130162 | GEO
Project description:In the present study we compare the effect of integrative and non-integrative strategies on pluripotency during pig somatic cells reprogramming to pluripotency. Microarray analysis was used to compare the gene expression profile of non reprogrammed porcine embryonic fibroblasts (PEF) and of iPS-like cells obtained by cell reprogramming of control amniocytes (PB20) or fibroblasts from animals carrying a t(Y;14) translocation (I, NI). We investigate the impact of different reprogramming techniques by using a first integrative method based on viral infection (PB20, I) and a second non-integrative method based on the use of Sendaï viruses (NI). Moreover, we analyzed the changes in gene expression profile upon embryoïd formation in the NI-iPS-like cells (EB). We cultured one cell line of porcine embryonic fibroblast, one cell line of iPS-like cells derived from normal amniocytes (PB20), 2 cell lines derived from t(Y;14) fibroblast by the integrative technique (I3 and I4) both at early (ep) and late passages (lp), and three cell lines derived from t(Y;14) fibroblasts by the non-integrative method (NI12, NI13 and NI20). Embryoïd bodies from NI cell lines were obtained by 10 days of floating culture in a specific medium under low agitation (EB12, EB13 and EB20). Total RNA from cell pellets of each sample was extracted in triplicate using the Nucleospin RNA kit (Macherey-Nagel) and checked for quantity and quality. After the microarrays experimentation, quality control and normalization, 34 over 36 samples were conserved (represented here).
2016-07-03 | E-GEOD-71792 | biostudies-arrayexpress