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TranscriptomicsGenomic characterization of ovarian cancer spheroids
Spheroids are 3D multi-cell aggregates formed in non-addherent culture conditions. In ovarian cancer (OC), they serve as a vehicle for cancer cell dissemination in the peritoneal cavity. We investigated genes and networks upregulated in three dimensional (3D) versus two-dimensional (2D) culture cond...
ORGANISM(S): Homo sapiens 
2014-01-03 | E-GEOD-53759 | biostudies-arrayexpress
ProteomicsDiesel particulate matter-induced proteomic changes in three-dimensional spheroids derived from human primary cells of various tissue origins
This study investigated the effects of diesel particulate matter (DPM) on multiple human organs using 3D spheroids derived from eight human primary cell types. To assess the impact of DPM, we exposed these spheroids to varying concentrations of standardized DPM (SRM 2975) and measured their viabilit...
ORGANISM(S): Homo sapiens (Human) 
2025-08-21 | PXD056979 | Pride
Three-dimensional (3d) spheroids Mass spectrometry (ms) Diesel particulate matter (dpm) Viability assessment Tandem mass tag (tmt) 
GenomicsTranscriptomic profiling of two-dimensional cultured cells and three-dimensional dental pulp stem cell spheroids regulated by spermidine and TGF-β3
Transcriptomic profiling of two-dimensional cultured cells and three-dimensional dental pulp stem cell spheroids regulated by spermidine and TGF-β3
PRJNA1508978 | ENA
ProteomicsAnimal product-free culture conditions for 3D primary human hepatocyte spheroids improve long-term viability and drug metabolism
3D cultures of primary human hepatocytes (3D PHH) are successfully used to reduce and replace the use of animal experiments in biomedical research. Yet, the initial formation of 3D PHH is highly dependent on the supplementation with fetal bovine serum (FBS). However, the molecular composition of FBS...
ORGANISM(S): Homo sapiens (Human) 
2026-01-23 | PXD056428 | Pride
Human Setum-free Fbs Liver 3d phh 
ProteomicsA Vascularized Three-Dimensional Breast Cancer Model: Mimicking the Tumor Microenvironment and Chemoresistance
Tumorigenesis is a complex and dynamic process in which the tumor microenvironment (TME) plays a central role. In solid tumors, the TME contributes to key mechanisms of tumor progression, including metastasis, immune evasion, and resistance to therapies. One major challenge in preclinical cancer res...
ORGANISM(S): Rattus norvegicus (Rat) 
2026-02-23 | PXD067876 | Pride
Angiogenesis  spheroids  microvascular fragments  tumor microenvironment  3d tumor model 
TranscriptomicsChanges in Global Gene Expression Associated with 3D Structure of Tumors: an ex vivo Matrix-Free Mesothelioma Spheroid Model
Tumor microenvironments present significant barriers to anti-tumor agents. Molecules involved in multicellular tumor microenvironments, however, are difficult to study ex vivo. Here, we generated a matrix-free tumor spheroid model using the NCI-H226 mesothelioma cell line and compared the gene expre...
ORGANISM(S): Homo sapiens 
2012-06-20 | E-GEOD-37629 | biostudies-arrayexpress
ProteomicsEfficient fabrication of human corneal stromal cell spheroids and promoting cell stemness based on 3D-printed derived PDMS microwell platform
Here, we introduce a novel three-dimensional (3D) cell culture system based on a pol-ydimethylsiloxane (PDMS) microwell platform composed of many V-bottom microcavities for the generation of human corneal stromal spheroids. We isolated hCSCs from SMILE-derived lenticules and maintained their physiol...
ORGANISM(S): Homo Sapiens 
2025-02-15 | PXD060857 |
GenomicsThree-Dimensional Matrix Stiffness Modulates Mechanosensitive and Phenotypic Alterations in Oral Squamous Cell Carcinoma Spheroids
Three-Dimensional Matrix Stiffness Modulates Mechanosensitive and Phenotypic Alterations in Oral Squamous Cell Carcinoma Spheroids
PRJNA1090463 | ENA
TranscriptomicsTranscriptomic profiling of two-dimensional cultured cells and three-dimensional dental pulp stem cell spheroids regulated by spermidine and TGF-β3
Dental pulp stem cells (DPSCs) exhibit distinct biological behaviors under conventional two-dimensional (2D) culture and three-dimensional (3D) spheroid conditions. To investigate the transcriptional regulation associated with spheroid formation and biomimetic factor-mediated functional modulation, ...
ORGANISM(S): Homo sapiens 
2026-08-11 | GSE342852 | GEO
ProteomicsProteomic characterisation of inducible proteins in three dimensional cultures
Three-dimensional models have gained significant traction over the past decade and are considered a powerful tool for improving the concordance between in vitro and in vivo phenotypes. However, the duration of spheroid culture may influence the degree of correlation between these counterparts. When ...
ORGANISM(S): Homo sapiens (Human) 
2021-05-26 | PXD024353 | Pride
Hepg2 Spheroids Proteomics 
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