Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA218628 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds. These scaffolds include polycaprolactone (PCL) nanofibers (PCL_NF), films (PCL_SC), poly D,L-lactic acid (PDLLA) nanofibers (PDLLA_NF), films (PDLLA_SC), tissue culture polystyrene (TCPS) and TCPS with osteogenic supplements (TCPS_OS). The results revealed that scaffold structure was able to significantly affect gene expression, with nanofiber scaffolds inducing similar gene expression patterns to hBMCSs cultured with osteogenic media. A library of scaffolds prepared from polycaprolactone or poly D,L-lactic acid was sythesized and cultured with hBMSCs for 14 days with RNA extracted from cells on Day 1 and Day 14. Gene expression analysis was performed using BRB ArrayTools. SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements. This data forms is part of a pending publication: Baker et al. Ontology Analysis of Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films and is a subset of the 72 array data referenced in ( Kumar et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape, Biomaterials (2011) 32, 9188-9196.) The 72 array data set is submitted separately to GEO as GSE50743.
2013-11-01 | E-GEOD-50744 | biostudies-arrayexpress
Project description:Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds. The results revealed that gene expression patterns of hBMSCs grouped according to scaffold. A library of scaffolds prepared from polycaprolactone (PCL) or poly D,L-lactic acid (PDLLA) was sythesized and cultured with hBMSCs for 14 days with RNA extracted from cells on Day 1 and Day 14. Gene expression analysis was performed using BRB ArrayTools. GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements. The 72 arrays data was used previously in the publication: Kumar et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape, Biomaterials (2011) 32, 9188-9196. A companion data set of 24 arrays was submitted separately to GEO as GSE50744 and will be referenced to Baker et al. Ontology Analysis of Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films
2013-11-01 | E-GEOD-50743 | biostudies-arrayexpress
Project description:Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds. These scaffolds include polycaprolactone (PCL) nanofibers (PCL_NF), films (PCL_SC), poly D,L-lactic acid (PDLLA) nanofibers (PDLLA_NF), films (PDLLA_SC), tissue culture polystyrene (TCPS) and TCPS with osteogenic supplements (TCPS_OS). The results revealed that scaffold structure was able to significantly affect gene expression, with nanofiber scaffolds inducing similar gene expression patterns to hBMCSs cultured with osteogenic media.
2013-11-01 | GSE50744 | GEO
Project description:Bulk RNA-seq data of 2D- vs. 3D-cultured human bone marrow stromal cells.
2024-09-15 | GSE184225 | GEO
Project description:Human bone marrow mesenchymal stromal cells (MSCs) are conventionally cultured as adherent monolayers on tissue culture plastic. MSCs can also be cultured as 3D cell aggregates (spheroids). Optimised 3D conditions (60,000 MSCs cultured as a spheroid for 5 days) inhibited MSC proliferation and induced cell shrinkage in the absence of cell death. Primary human MSCs isolated from 2 donors were cultured under both monolayer (2D MSCs) and optimised 3D (3D MSCs) conditions. High quality RNA was isolated from all samples, and global gene expression analysis was performed in duplicate (using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays) to identify gene expression changes in 3D compared to 2D MSC cultures.
2015-09-30 | E-MTAB-3795 | biostudies-arrayexpress
Project description:RNA and ATAC sequencing data of primary sorting CD45-Ter119-CD31-Scf; GFP+Cxcl12; DsRed+ bone marrow stromal cells ,2D cultured bone marrow stromal cells and 3D cultured bone marrow stromal cells. RNA sequencing data of sorted primary and 3D cocultured Lin-Sca1+C-kit+CD150+CD48+ hematopoietic stem cells from 8-12 weeks and 12-13 months old mice. RNA and ATAC sequencing data of primary sorting CD45-Ter119-CD31-Pdgfra+td-Tomato+ bone marrow stromal cells from young (8 wks), middle aged (12 months) and aged (22-24 months) Lepr-Cre;td-Tomato mice.
2023-04-06 | GSE180866 | GEO
Project description:The unique properties of the bone marrow allow for migration and proliferation of multipl myeloma (MM) cells, while also providing the perfect environment for development of quiescent, drug-resistant MM cell clones. Bone marrow adipocytes (BMAds), which have recently been identified as important contributors to systemic adipokine levels, bone strength, hematopoiesis, and progression of metastatic and primary bone marrow cancers, such as MM. Recent studies in myeloma suggest that BMAds can be reprogrammed by tumor cells to contribute to myeloma-induced bone disease, and reciprocally, BMAds support MM cells in vitro. Importantly, most data investigating BMAds have been generated using adipocytes derived by differentiating bone marrow-derived mesenchymal stromal cells (MSCs) into adipocytes in vitro using adipogenic media, due to the extreme technical challenges associated with isolating and culturing primary adipocytes. However, if studies could be performed with primary adipocytes, they likely will recapitulate in vivo biology better than MSC-derived adipocyte, as the differentiation process is artificial and differs from in vivo differentiation, and progenitor cell(s) of the primary BMAd may not be the same as the MSCs precursors used for adipogenic differentiation in vitro. Therefore, we developed and refined three methods for culturing primary BMAds (pBMAds): 2D coverslips, 2D transwells, and 3D silk scaffolds, all of which can be cultured alone or with MM cells to investigate bidirectional tumor-host signaling. To develop an in vitro model with a tissue-like structure to mimic the bone marrow microenvironment, we developed the first 3D, tissue engineered model utilizing pBMAds derived from human bone marrow. We found that pBMAds, which are extremely fragile, can be isolated and stably cultured in 2D for 10 days and in 3D for short term (~2 weeks) or long term (1 month) in vitro. To investigate the relationship between pBMAds and myeloma, MM cells can be added to investigate physical relationships through confocal imaging and soluble signaling molecules via mass spectrometry. In sum, we developed three in vitro cell culture systems to study primary bone marrow adipocytes and myeloma cells, which could be adapted to investigate many diseases and biological processes involving the bone marrow, including other bone-homing tumor types.
2023-01-04 | PXD032753 | Pride
Project description:A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheres (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level Neural progenitor cells were cultured on 2D surfaces, in 3D scaffolds and as 3D neural spheres. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared.
2009-12-22 | E-GEOD-13715 | biostudies-arrayexpress
Project description:Development of systems allowing the maintenance of native properties of mesenchymal stromal cells (MSC) is a critical challenge for studying physiological functions of skeletal progenitors, as well as towards cellular therapy and regenerative medicine applications. Conventional stem cell culture in monolayer on plastic dishes (2D) is associated with progressive loss of functionality, likely due to the absence of a biomimetic microenvironment and the selection of adherent populations. Here we demonstrate that 2D MSC expansion can be entirely bypassed by culturing freshly isolated bone marrow cells within the pores of 3D scaffolds in a perfusion-based bioreactor system, followed by enzymatic digestion for cell retrieval. The 3D-perfusion system supported MSC growth while maintaining cells of the hematopoietic lineage, and thus generated a cellular environment mimicking some features of the bone marrow stroma. As compared to 2D-expansion, sorted CD45- cells derived from 3D-perfusion culture after the same time (3 weeks) or a similar extent of proliferation (7-8 doublings) maintained a 4.3-fold higher clonogenicity and exhibited a superior differentiation capacity towards all typical mesenchymal lineages, with similar immunomodulatory function in vitro. Transcriptomic analysis performed on MSC from 5 donors validated the robustness of the process and indicated a reduced inter-donor variability as well as a significant upregulation of multipotency-related gene clusters following 3D-perfusion as compared to 2D expansion. The described system offers a model to study how factors of a 3D engineered niche may regulate MSC function and, by streamlining conventional labor-intensive processes, is prone to automation and scalability within closed bioreactor systems. Nucleated cells were isolated from 5 fresh human bone marrow aspirates by means of red blood cells lyses buffer and then were seeded into a 3D perfusion bioreactor system using a pure hydroxyapatite 3D scaffold and in conventional Petri dishes (2D). After culture for 19 days, cells from both systems were enzymatically retrieved and sorted using anti-CD45-coated magnetic beads. Total RNA was extracted from CD45- cells, QCed and hybridized to Affymetrix microarrays.
2014-08-01 | E-GEOD-52896 | biostudies-arrayexpress
Project description:A transcriptomic expression comparison was done among superior cervical ganglion (SCG) cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and in freshly dissected tissue (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level SCG cells were cultured on 2D surfaces and in 3D scaffolds. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared. Cells from freshly dissected tissue were used as in vivo surrogates for positive control of 3D cells.
2012-07-06 | E-GEOD-30498 | biostudies-arrayexpress