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Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with 20 uM Carnosic Acid

ABSTRACT: Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with 20 uM Carnosic Acid

PROVIDER: PRJNA949643 | ENA |

REPOSITORIES: ENA

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Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with 20 uM Carnosic Acid

Project description:Gene expression profiling reveals multiple tissue-specific functionality of carnosic acid in a stem-based tool. We evaluated the effects of carnosic acid on human amniotic epithelial stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of carnosic acid in a stem cell-based tool.

2023-04-02 | GSE228408 | GEO

Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with Tsuruazuki Extract (Tsuru)

Project description:Gene expression profiling reveals mesoderm lineage-specific genes were more significantly regulated with the most prominent regulated DEGs were identified in adipose tissue. We evaluated the effects of Tsuruazuki extract on human amniotic epithelial stem cells. We performed an untargeted whole-genome transcriptome analysis to explore functionality of Tsuru in a stem cell-based tool.

2024-09-30 | GSE278052 | GEO

Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with Tsuruazuki Extract (Tsuru)

Project description:Gene expression data from 3D spheroids of human amniotic epithelial stem cell (hAESC) treated with Tsuruazuki Extract (Tsuru)

| PRJNA1165280 | ENA

Generating mesenchymal stem cells in 3D from human embryonic stem cell spheroids

Project description:Background: Mesenchymal stem cells (MSC) derived from human embryonic stem cells (hESC), named EMSC here, have been found efficacious in animal models of autoimmune, inflammatory, and degenerative diseases. However, all the EMSC derivation methods reported so far are in two-dimensional (2D) culture systems, which are of low efficiency and high cost, difficult for large-scale production for research and therapeutic applications. Methods: We established a 3D system that allowed differentiation of hESC spheroids into MSC spheroids (EMSCSp) following treatment with BMP4 and A8301 for 5 days and subsequent culture in a MSC medium for about 15 days. All the procedures were conducted in one vessel without intermediate passaging. Results: EMSCsp cells were efficiently derived from hESC spheroids within 20 days in the 3D culture system, which could be scaled up from a small culture vessel to a 100-ml plastic bag. EMSCSp could further differentiate into spheroids of chondrocytes or adipocytes. EMSCSp could also reattach and form a 2D-monolayer culture (EMSCSp-ML). Compared to EMSC differentiated in monolayer, EMSCSp-ML had faster proliferation and higher yield, and developed less apoptosis and slower senescence. EMSCSp-ML also retained immune-modulatory effects in vitro and therapeutic effects on two mouse models of colitis. Conclusions: The 3D method provides a simple and economic system for large-scale production of EMSC as an unlimited source of the therapeutically promising cells.

2018-07-03 | GSE93218 | GEO

Maturation of Human iPSC-derived Astrocytes in 3D Cortical Spheroids

Project description:Single-cell RNA-seq: We used single-cell RNAseq to investigate the maturation of astrocytes within human cortical spheroids Bulk RNA-seq: Bulk sequencing from astrocytes and neurons purified (via immunopanning) from iPSC-derived coritical spheroids at varying in vitro differentiation states

2017-07-31 | GSE99951 | GEO

Mechanical cues guide the formation and patterning of 3D spheroids in fibrous environments

Project description:Multicellular spheroids have shown great promise in 3D biology. Many techniques exist to form spheroids, but how cells take mechanical advantage of native fibrous extracellular matrix (ECM) to form spheroids remains incompletely understood. Here, we identify the role of fiber diameter, architecture, and contractility on spheroids' spontaneous formation, growth, and maintenance using ECM-mimicking fiber networks. We show that matrix deformability is critical to forming spheroids, with deformable aligned fiber networks promoting spheroid formation independent of fiber diameter, while larger-diameter crosshatched networks of low deformability abrogate spheroid formation. Thus, a mixture of diameters and architectures allowed spatial patterning of spheroids and monolayers simultaneously. We quantify the forces involved during spheroid formation and identify the contractile role of Rho-associated protein kinase (ROCK) in spheroid formation and maintenance. Interestingly, we observed spheroid-spheroid and multiple spheroid mergers, which we describe by spheroid-shape-driven morphogenic Boolean outcomes. We found that spheroid mergers were initiated by exchanging a few cells and forming a cellular bridge connecting the two spheroids. Unexpectedly, we found large pericyte spheroids contract rhythmically. Overall, we ascertained that contractility and network deformability work together to spontaneously form and pattern 3D spheroids, potentially connecting in vivo matrix biology with developmental, disease, and regenerative biology.

2025-08-05 | GSE284140 | GEO

Denunded HUVEC/HUASMC spheroids vs. HUASMC spheroids

Project description:Denunded HUVEC/HUASMC spheroids vs. HUASMC spheroids

| PRJNA657248 | ENA

Barcode and Whole Exome Sequencing Data of Dabrafenib Resistant 3D-HT-29 and Irinotecan Resistant 3D-HCT-116 Spheroids

Project description:HT-29 and HCT-116 cells were barcoded using the CloneTracker lentiviral barcode library and then dabrafenib and irinotecan resistant derivatives of these cell lines were established, respectively.10 million barcoded HT-29 and HCT-116 cells were seeded equally onto poly-HEMA coated 4xT75 flask (DMSO Control, Replica A, B, C for each drug). After seeding, cells were allowed to form spheroids and barcoded 3D-HT-29 spheroids were treated with dabrafenib at increasing doses starting from IC50/10 dose until IC50/2 dose with monthly doubling of the dosing (16 weeks), and barcoded 3D-HCT-116 cells were treated with irinotecan at increasing doses starting from IC50/4 dose until IC50 dose with weekly doubling of the dosing (4 weeks). Following the end points of treatment for each cell line, DNA was isolated from harvested cell lines and barcode sequencing and whole exome sequencing were carried out.

2023-09-01 | E-MTAB-13216 | biostudies-arrayexpress

Project description:metabolite levels provided by UM platform (Creative Dynamics Inc, NY, USA) (the data is raw abundance. Mapping was applied on log10 transformed data)

| EGAD00010002146 | EGA

Transcriptomic profile of 3D spheroids developed from Astyanax Liver-derived cells - SFL and CFL.

Project description:Liver-derived cells from the surface and cave-adapted morphs of Astyanax mexicanus are valuable in vitro resources to explore the metabolism of these unique fish. However, 2D cultures have not yet fully mimicked the metabolic profile of the fish liver. Also, 3D culturing can modulate the transcriptomic profile of cells when compared to its 2D counterpart. Hence, to widen the range of metabolic pathways that can be depicted in vitro, we cultured the liver-derived SFL and CFL into 3D spheroids. We 3D cultured the cells at various cell seeding densities for 4 weeks and characterized the resultant transcriptome. The 3D cultured SFL and CFL cells indeed depicted a wider range of metabolic pathways as compared to the 2D culture. Further, the 3D spheroids also showed surface and cave-specific responses, making the spheroids an exciting system to study cave adaptation. Taken together, SFL and CFL spheroids prove to be a promising model for overall understanding of altered metabolism in Astyanax mexicanus.

2023-06-13 | GSE234212 | GEO

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