High resolution 3D mapping of cellular heterogeneity within multiple types of mineralized tissues
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1139880 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:High resolution 3D mapping of cellular heterogeneity within multiple types of mineralized tissues
| PRJNA1139879 | ENA
Project description:Organic P mineralized bacteria Raw sequence reads
| PRJNA1061378 | ENA
Project description:We examine the transcriptional alterations induced by in vitro culture of MDA-MB-231 cells on microfabricated hydroxyapatite-mineralized collagen devices that simulate bone matrix (PMID 29759731). As a control, we additionally characterize the transcriptional activity of cells cultured on a collagen substrate. We find that mineralized collagen increases the expression of genes associated with stemness and metastasis while culture on collagen increased expression of genes associated with cell cycle progression.
2023-07-19 | GSE229094 | GEO
Project description:Biodegradable plastics are one possible solution for reducing plastic waste, yet the mechanisms and organisms involved in their degradation in the aquatic environment remain understudied. In this study, we have enriched a microbial community from North Sea water and sediment, capable of growing on the polyester poly(butylene succinate). This culture was grown on two other biodegradable polyesters, polycaprolactone and ecovio® FT (a PBAT-based blended biodegradable plastic), and the differences between community structure and activity on these three polymers were determined by metagenomics and metaproteomics. We have seen that the plastic supplied drives the community structure and activity. Setups growing on ecovio® FT were more diverse, yet showed the lowest degradation, while poly(butylene succinate) and polycaprolactone resulted in a less diverse community but much higher degradation efficiencies. The dominating species were Alcanivorax sp., Thalassobius sp., or Pseudomonas sp., depending on the polymer supplied. Furthermore, we have observed that Gammaproteobacteria were more abundant and active within the biofilm and Alphaproteobacteria within the free-living fraction of the enrichments. Two of the three PETase-like enzymes isolated were expressed as tandems (Ple -tan1 &Ple – tan2) and all three were produced by Pseudomonas sp. Of those, Ple-tan1 was most active on all three substrates and also the most thermostable. Overall, we could show that all three plastics investigated can be mineralized by bacteria naturally occurring within the marine environment and characterize some of the enzymes involved in the degradation process.
2023-11-22 | PXD038098 | Pride
Project description:The tumor microenvironment consists of resident tumor cells organized within a compositionally diverse, three-dimensional (3D) extracellular matrix (ECM) network that cannot be replicated in vitro using bottom-up synthesis. We report a new self-assembly system to engineer ECM-rich 3D MatriSpheres wherein tumor cells actively organize and concentrate microgram quantities of decellularized ECM dispersions which modulate cell phenotype. 3D colorectal cancer (CRC) MatriSpheres were created using decellularized small intestine submucosa (SIS) as an orthotopic ECM source that had greater proteomic homology to CRC tumor ECM than traditional ECM formulations such as Matrigel. SIS ECM was rapidly concentrated from its environment and assembled into ECM-rich 3D stroma-like regions by mouse and human CRC cell lines within 4-5 days via a mechanism that was rheologically distinct from bulk hydrogel formation. Both ECM organization and transcriptional regulation by 3D ECM cues affected programs of malignancy, lipid metabolism, and immunoregulation that corresponded with an in vivo MC38 tumor cell subpopulation identified via single cell RNA sequencing. This 3D modeling approach stimulates tumor specific tissue morphogenesis that incorporates the complexities of both cancer cell and ECM compartments in a scalable, spontaneous assembly process that may further facilitate precision medicine.
2024-05-03 | MSV000094671 | MassIVE
Project description:Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes. Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells.
2019-02-27 | GSE116869 | GEO
Project description:Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes. Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells.
2019-02-27 | GSE116872 | GEO
Project description:Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes. Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells.
2019-02-27 | GSE116875 | GEO
Project description:Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes. Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells.
2019-02-27 | GSE116874 | GEO
Project description:Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes. Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells.
2019-02-27 | GSE116870 | GEO