Ontology highlight
ABSTRACT:
PROVIDER: PRJNA561962 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10019100_1.fastq.gz | Fastqsanger.gz | |||
| SRR10019100_2.fastq.gz | Fastqsanger.gz | |||
| SRR10019101_1.fastq.gz | Fastqsanger.gz | |||
| SRR10019101_2.fastq.gz | Fastqsanger.gz | |||
| SRR10019102_1.fastq.gz | Fastqsanger.gz |
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Project description:Colonies of induced pluripotent stem cells (iPSCs) reveal aspects of self-organization even under culture conditions that maintain pluripotent state. To investigate the dynamics of this process under spatial confinement we used either PDMS pillars or micro-contact printing of vitronectin. OCT4, E-cadherin, and NANOG were progressively upregulated within about 70 µm from the outer rim of iPSC colonies. Single-cell RNA-sequencing demonstrated that OCT4high subsets have pronounced up-regulation of the TGF-β pathway, particularly of NODAL and its inhibitor LEFTY, at the rim of the colonies. Furthermore, calcium-dependent cell-cell interaction seemed to be relevant for the self-organization. After 5 to 7 days, the iPSC colonies detached spontaneously from micro-contact printed substrates to form 3D aggregates. This new method allowed generation of embryoid bodies (EBs) of controlled size, without any enzymatic or mechanical treatment. Within the early 3D aggregates, the radial organization and differential gene expression continued in analogy to the changes observed during self-organization of flat iPSC colonies. Our results provide further insight into the gradual self-organization within iPSC colonies and at their transition into EBs.
2022-08-26 | GSE184603 | GEO
Project description:Colonies of induced pluripotent stem cells (iPSCs) reveal aspects of self-organization even under culture conditions that maintain pluripotent state. To investigate the dynamics of this process under spatial confinement we used either PDMS pillars or micro-contact printing of vitronectin. OCT4, E-cadherin, and NANOG were progressively upregulated within about 70 µm from the outer rim of iPSC colonies. Single-cell RNA-sequencing demonstrated that OCT4high subsets have pronounced up-regulation of the TGF-β pathway, particularly of NODAL and its inhibitor LEFTY, at the rim of the colonies. Furthermore, calcium-dependent cell-cell interaction seemed to be relevant for the self-organization. After 5 to 7 days, the iPSC colonies detached spontaneously from micro-contact printed substrates to form 3D aggregates. This new method allowed generation of embryoid bodies (EBs) of controlled size, without any enzymatic or mechanical treatment. Within the early 3D aggregates, the radial organization and differential gene expression continued in analogy to the changes observed during self-organization of flat iPSC colonies. Our results provide further insight into the gradual self-organization within iPSC colonies and at their transition into EBs.
2022-08-26 | GSE160665 | GEO
Project description:Using 4C-Seq experimental procedure we have characterized, in cultured chicken lymphoid and erythroid cells, genome-wide patterns of spatial contacts of several CpG islands scattered along the chromosome 14. A clear tendency for interaction of CpG islands present within the same and different chromosomes has been observed. Accordingly, preferential spatial contacts between Sp1 binding motifs, and other GC-rich genomic elements including DNA sequence motifs capable to form G-quadruplexes were demonstrated. On the other hand, an anchor placed in gene/CpG islands-poor area was found to form spatial contacts with other gene/CpG islands-poor areas within chromosome 14 and other chromosomes. These results corroborate the two compartments model of interphase chromosome spatial organization and suggest that clustering of CpG islands harboring promoters and origins of DNA replication constitutes an important determinant of the 3D organization of eukaryotic genome in the cell nucleus. Using ChIP-Seq experimental procedure we have mapped genome-wide the CTCF deposition sites in chicken lymphoid and erythroid cells subjected to the 4C analysis. A good correlation between the density of these sites and the level of 4C signals was observed for the anchors located in CpG islands. It is thus possible that CTCF contributes to the clustering of CpG islands revealed in our experiments. Using ChIP-Seq experimental procedure we have mapped genome-wide the CTCF deposition sites in chicken lymphoid and erythroid cells subjected to the 4C analysis. CTCF deposition sites in chicken lymphoid and erythroid (induced and non-induced) cells.
2014-03-01 | E-GEOD-51846 | biostudies-arrayexpress
Project description:This is the scaled model described in the article:
Birhythmicity, chaos, and other patterns of temporal self-organization in a multiply regulated biochemical system
Olivier Decroly, Albert Goldbeter, Proc Natl Acad Sci USA 1982 79:6917-6921; PMID:6960354;
Abstract:
We analyze on a model biochemical system the effect of a coupling between two instability-generating mechanisms. The system considered is that of two allosteric enzymes coupled in series and activated by their respective products. In addition to simple periodic oscillations, the system can exhibit a variety of new modes of dynamic behavior; coexistence between two stable periodic regimes (birhythmicity), random oscillations (chaos), and coexistence of a stable periodic regime with a stable steady state (hard excitation) or with chaos. The relationship between these patterns of temporal self-organization is analyzed as a function of the control parameters of the model. Chaos and birhythmicity appear to be rare events in comparison with simple periodic behavior. We discuss the relevance of these results with respect to the regularity of most biological rhythms.
The parameters q1 = 50 and q2 = 0.02 are explicitely included as the stoichiometric coefficients of beta and gamma in the reactions r2 and r3, respectively. Parameter values and initial conditions [ks=1.99/sec, alpha(0)=29.19988, beta(0)=188.8, gamma(0)=0.3367] are for the chaotic regime presented in the upper-curve of Figure 3b.
2024-09-02 | BIOMD0000000319 | BioModels
Project description:The small intestinal crypt exhibits a defined spatial organisation involving multiple cell types that undergo continuous proliferation and differentiation while migrating towards the villus. We have built a multi-scale agent-based model (ABM), with individual cells interacting in the crypt geometry, which reproduces the self-organizing stable behaviour reported for the crypt. In our ABM, spatial organization emerges from the dynamic interaction of multiple signalling pathways, which include the Wnt, Notch, BMP and RNF43/ZNRF3 pathways that orchestrate cellular fate and mechanisms of contact inhibition of proliferation as well as feedback loops that regulate the expansion of the niche and size of the crypt. Moreover, this dynamic signalling network interacts with the main cell cycle proteins, governing the progression of each cell across the division stages.
2024-11-22 | MODEL2212120002 | BioModels
Project description:Tissue function relies on the precise spatial organization of cells characterized by distinct molecular profiles. Single-cell RNA-Seq captures molecular profiles but not spatial organization. Conversely, spatial profiling assays to date have lacked global transcriptome information, throughput or single-cell resolution. Here, we develop High-Density Spatial Transcriptomics (HDST), a method for RNA-Seq at high spatial resolution. Spatially barcoded reverse transcription oligonucleotides are coupled to beads that are randomly deposited into tightly packed individual microsized wells on a slide. The position of each bead is decoded with sequential hybridization using complementary oligonucleotides providing a unique bead-specific spatial address. We then capture, and spatially in situ barcode, RNA from the histological tissue sections placed on the HDST array. HDST recovers hundreds of thousands of transcript-coupled spatial barcodes per experiment at 2 μm resolution. We demonstrate HDST in the mouse brain, use it to resolve spatial expression patterns and cell types, and show how to combine it with histological stains to relate expression patterns to tissue architecture and anatomy. HDST opens the way to spatial analysis of tissues at high resolution.
2019-09-09 | GSE130682 | GEO
Project description:Each protein within a regulatory complex associates with the genome by either binding DNA directly or by forming protein-protein interactions with DNA-bound proteins. In the chromatin immunoprecipitation (ChIP) assay, each protein’s unique mode of genomic association may be reflected by their patterns of formaldehyde-induced crosslinks to the DNA sequences that are in very close proximity. The ChIP-exo protocol precisely delineates protein-DNA crosslinking patterns by combining ChIP with 5' to 3' exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to the DNA affects crosslinking efficiencies. Therefore, the spatial organization of a protein-DNA complex could potentially be inferred by analyzing how crosslinking signatures vary between the subunits of a regulatory complex, and how they remain consistent over a set of coordinately regulated regions. Here, we present a computational framework that aligns ChIP-exo crosslinking patterns from multiple proteins across a set of regulatory regions, and which detects and quantifies protein-DNA crosslinking events within the aligned profiles. Our gapped multiple profile alignment approach does not rely on sequence motif features, but rather operates directly on the multi-protein, strand separated ChIP-exo tag patterns. The output of the alignment approach is a set of composite profiles that represent the crosslinking signatures of the complex across analyzed regulatory regions. We then use a probabilistic mixture model to deconvolve individual crosslinking events within the aligned ChIP-exo profiles, enabling consistent measurements of protein-DNA crosslinking strengths across multiple proteins. Lastly, we apply dimensionality reduction to visualize the relative organization of proteins within the regulatory complex. We demonstrate our approach by applying it to characterize regulatory complex organization in three biological settings. Firstly, we demonstrate that our alignment approach can recover the known organization of regulatory proteins at yeast ribosomal protein genes, without relying on any DNA sequence features. Secondly, we apply our gapped alignment and crosslinking quantification approaches to a novel set of ChIP-exo data to characterize the spatial organization of Pol III transcriptional machinery assembly at yeast tRNA genes. Finally, we demonstrate that our approach can be used to quantify changes in protein-DNA complex organization when applied to ChIP-nexus data from Drosophila Pol II transcriptional components in two experimental conditions. Our results suggest that principled analyses of ChIP-exo crosslinking patterns enable inference of spatial organization within protein-DNA complexes.
2019-12-08 | GSE140923 | GEO
Project description:The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates
| PRJNA765340 | ENA
Project description:We have correlated transciptomics, proteomics and toponomics analyses of hippocampus tissue of inbred C57/BL6 mice to analyse the interrelationship of expressed genes and proteins at different levels of organization. We find that transcriptome and proteome levels of function are highly conserved between different mice, while the topological organization (the toponome) of protein clusters in synapses of the hippocampus is highly individual, with only few interindividual overlaps (0.15 %). In striking contrast, the overall spatial patterns of individual synaptic states, defined by protein clusters, have boundaries within a strict and non-individual spatial frame of the total synaptic network. The findings are the first to provide insight in the systems biology of gene expression on transcriptome, proteome and toponome levels of function in the same brain subregion. The approach may lay the ground for designing studies of neurodegeneration in mouse models and human brains. Experiment Overall Design: 4 biological replicates, all wild type
2008-06-19 | E-GEOD-8239 | biostudies-arrayexpress
Project description:Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Our time-resolved RNA-sequencing and live-cell super-resolution imaging experiments revealed a physiological consequence of this spatial organization and the underlying mechanism: membrane localization enhances degradation rates of inner-membrane-protein mRNAs by placing them in proximity to membrane-bound RNA degradation enzymes. Together, these results demonstrate that the bacterial transcriptome is spatially organized and that this organization shapes the posttranscriptional Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Our time-resolved RNA-sequencing and live-cell super-resolution imaging experiments revealed a physiological consequence of this spatial organization and the underlying mechanism: membrane localization enhances degradation rates of inner-membrane-protein mRNAs by placing them in proximity to membrane-bound RNA degradation enzymes. Together, these results demonstrate that the bacterial transcriptome is spatially organized and that this organization shapes the post-transcriptional dynamics of mRNAs.
2016-06-07 | GSE75818 | GEO