Similar Datasets
Project description:scRNA-seq of mouse prostate 2D and 3D organoids
| PRJNA1151063 | ENA
Project description:* To compare surgical and oncological outcomes in patients underwent to colorectal resection with 3D vs 2D laparoscopic technique.
* To evaluate the visual overload in surgeons using 3D laparoscopic technique.
| 2220465 | ecrin-mdr-crc
Project description:Kidney organoids differentiated from human pluripotent stem cells are complex structures that capture glomerular, tubular and mesenchymal cell types of the developing human kidney. The STEMdiff™ Kidney Organoid Kit is a serum-free cell culture medium system for the efficient and reproducible generation of kidney organoids in 2D using a simple, 18 day, two-stage differentiation protocol. We recently also showed compatibility of this kit for the generation of 3D organoids using single cell dissociation and re-aggregation on Day 7. Here we evaluate kidney organoids derived from the commercially available hiPSC line SCTi004-A with the STEMdiff™ Kidney Organoid Kit for their cellular diversity and transcriptomic profiles. Datasets were created for kidney organoids differentiated in the 2D and 3D format.
2025-12-09 | GSE312980 | GEO
Project description:Kidney organoids are ideal models to study the complex process of human kidney development. Here we report the generation of functional kidney organoids by reprogramming human urine epithelial cells (hUCs). RNA-seq and ATAC-seq revealed the three-stage process of the 2D U-iRO induction. Single cell RNA-seq further reveals the cell types in 2D and 3D organoids, 2D U-iRO dominated with mesenchyme and 3D U-iRO with tubule.
2022-10-18 | GSE198840 | GEO
Project description:Interventions: 2D group:2D laparoscopic surgery;3D group:3D laparoscopic surgery
Primary outcome(s): operation time;The amount of bleeding;Number of lymph nodes;Postoperative gastrointestinal function recovery time;Postoperative complications
Study Design: Randomized parallel controlled trial
| 2663755 | ecrin-mdr-crc
Project description:Two-dimensional (2D) culture models are commonly used in cancer research, but fail to recapitulate complex mechanical cues of native tissues. In this study, we developed an ex vivo three-dimensional (3D) lung cancer model by seeding human lung adenocarcinoma cells into decellularised rat lungs and culturing them in a pressure chamber and perfusion system mimicking respiratory motion (RM) and blood flow. In 3D culture, RM promoted cell adhesion and proliferation, enhanced the nuclear translocation of β-catenin and YAP, and increased the expression of integrin β1 and E-cadherin. In addition, upregulation of extracellular matrix- and cell adhesion-related genes was particularly notable. In contrast, in 2D culture, RM suppressed cell proliferation and induced apoptosis, with prominent upregulation of tumour suppressor genes. Our findings demonstrate that dimensionality and mechanical stress synergistically influence lung cancer cell dynamics and underscore the need for 3D models in cancer research that closely replicate the native lung tissue microenvironment.
2025-10-16 | GSE309015 | GEO
Project description:Two-dimensional (2D) culture models are commonly used in cancer research, but fail to recapitulate complex mechanical cues of native tissues. In this study, we developed an ex vivo three-dimensional (3D) lung cancer model by seeding human lung adenocarcinoma cells into decellularised rat lungs and culturing them in a pressure chamber and perfusion system mimicking respiratory motion (RM) and blood flow. In 3D culture, RM promoted cell adhesion and proliferation, enhanced the nuclear translocation of β-catenin and YAP, and increased the expression of integrin β1 and E-cadherin. In addition, upregulation of extracellular matrix- and cell adhesion-related genes was particularly notable. In contrast, in 2D culture, RM suppressed cell proliferation and induced apoptosis, with prominent upregulation of tumour suppressor genes. Our findings demonstrate that dimensionality and mechanical stress synergistically influence lung cancer cell dynamics and underscore the need for 3D models in cancer research that closely replicate the native lung tissue microenvironment.
2025-10-16 | GSE309016 | GEO
Project description:Background: Prostate cancer is the second leading cause of cancer mortality among US men. Epidemiological evidence suggests that high vitamin D status protects men from prostate cancer and the active form of vitamin D, 1α,25 dihydroxyvitamin D3 (1,25(OH)2D) has anti-cancer effects in cultured prostate cells. Still, the molecular mechanisms and the gene targets for vitamin D-mediated prostate cancer prevention are unknown. Results: We examined the effect of 1,25(OH)2D (+/- 100 nM, 6, 24, 48 h) on the transcript profile of proliferating RWPE1 cells, an immortalized, non-tumorigenic prostate epithelial cell line that is growth arrested by 1,25(OH)2D (Affymetrix U133 Plus 2.0, n=4/treatment per time and dose). Our analysis revealed many transcript level changes at a 5% false detection rate: 6 h, 1571 (61% up), 24 h, 1816 (60 % up), 48 h, 3566 (38 % up). 288 transcripts were regulated similarly at all time points (182 up, 80 down) and many of the promoters for these transcripts contained putative vitamin D response elements. Functional analysis by pathway or Gene Set Analysis revealed early suppression of WNT, Notch, NF-kB, and IGF1 signaling. Transcripts related to inflammation were suppressed at 6 h (e.g. IL-1 pathway) and suppression of proinflammatory pathways continued at later time points (e.g. IL-17 and IL-6 pathways). There was also evidence for induction of anti-angiogenic pathways and induction of transcripts for protection from oxidative stress or maintenance of cell redox homeostasis at 6 h. Conclusions: Our data reveal of large number of potential new, direct vitamin D target genes relevant to prostate cancer prevention. In addition, our data suggests that rather than having a single strong regulatory effect, vitamin D orchestrates a pattern of changes within prostate epithelial cells that limit or slow carcinogenesis. Experiment Overall Design: RWPE1 cells were treated with medium containing 100 nM of 1,25(OH)2D or vehicle (0.1% ethanol) for 6, 24 or 48 hours (n=4 per treatment, 24 total samples). The transcripts levels in each sample were measured by using the Affymetrix HU133 plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
2010-01-19 | E-GEOD-15947 | biostudies-arrayexpress
Project description:Expression data from HepG2 cultured in 2D monolayer cultures and 3D Matrigel cultures We performed this study to understand differences in gene expression profiles of 2D and 3D HepG2 cultures
2019-08-31 | GSE128763 | GEO
Project description:M21 or M21L cells were grown either in 2d (on plastic) or in a 3d-collagen model. 2x2 design, in triplicate
2012-07-10 | E-GEOD-34219 | biostudies-arrayexpress