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ShareScore release 0.9.0
Dataset results
146 results for “3D cell cultures”
Correlative microscopy of rat cultured hippocampal pyramidal cell from 40x confocal imaging to super-resolution 93x 3D STED of dendritic spines
<p>This dataset contain multi-scale image of rat hippocampal pyramidal cell related to our paper "<em>From tissues to segmentation: a modular framework for multi-scale neuron isolation</em>" by Cauzzo et al. <strong>Nature Comm (2024).</strong></p>
Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking
<p>Accompaning data to the paper:</p> <p>Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking</p>
Remotely controlled 3D-engineered scaffolds for biomimetic in vitro investigations on brain cell co-cultures
Open the record for dataset details and reuse information.
Driving cell response through deep learning, a study in simulated 3D cell cultures
Open the record for dataset details and reuse information.
Supplementary Videos S1-S2 3D co-culture spheroid formation containing A498-ST cells
<p><strong>Supplementary Videos S1-S2</strong></p> <p><strong>3D co-culture spheroid formation containing A498-ST cells </strong></p> <p>Representative movies (<strong>S1</strong>, bright field and <strong>S2,</strong> fluorescence stained) recorded for 24 hours of an A498-ST 3D co-culture capturing the kinetic formation of a 3D spheroid. 3D co-cultures harbor 70% tumor cells (A498-ST, green), 20% fibroblasts (NHDFα, blue) and 10% endothelial cells (ECRF24, red). Scalebar represents 1000 µm. </p>
Culturing Patient-Derived Malignant Hematopoietic Stem Cells in Engineered and Fully Humanized 3D Niches
<p>Data underlying the figures in the publication “Culturing patient-derived malignant hematopoietic stem cells in engineered and fully humanized 3D niches”, published in <em>PNAS,</em><em> <strong>2021</strong>, 118 (40) e2114227118.</em></p> <p><em>DOI: 10.1073/pnas.2114227118</em></p> <p>Table of contents:</p> <p><strong>1. AML data_Gene expression</strong>: qPCR data related to AML samples.</p> <p><strong>2. AML data_Protein</strong>: Luminex data related to AML samples.</p> <p><strong>3. AML data_Supernatant vs Niche</strong>: FACS data comparing AML cells in the supernatant and niche compartments.</p> <p><strong>4. AML data_Supernatant</strong>: FACS data showing AML cells in the supernatant along the time.</p> <p><strong>5. Chemotherapy_2D_FACS</strong>: FACS data showing leukemic cell viability in 2D.</p> <p><strong>6. Chemotherapy_3D_FACS</strong>: FACS data showing leukemic cell viability in 3D (engineered niches).</p> <p><strong>7. MPN data</strong>: FACS data related to MPN samples.</p> <p><strong>8. SV-N_FACS</strong>: FACS data characterizing SV-N.</p> <p><strong>9. SV-N_Gene expression</strong>: qPCR data characterizing SV-N.</p> <p><strong>10. UCSD-AML1_Niche_FACS</strong>: FACS data showing UCSD-AML1 cells in the niche at final analysis.</p> <p><strong>11. UCSD-AML1_Niche_Gene expression</strong>: qPCR data showing UCSD-AML1 cells in the niche at final analysis.</p> <p><strong>12. UCSD-AML1_Supernatant_FACS</strong>: FACS data showing UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>13. UCSD-AML1_Supernatant_Gene expression</strong>: qPCR data related to UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>14. UCSD-AML1_Supernatant_Protein</strong>: Luminex data related to UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>15. Images engineered niches</strong>: Zip archive containing images of engineered niches.</p>
Fig. 7. Superimposed 3D in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 7. Superimposed 3D structure of HRP-C (in brown) on A) 1AP2 and B) POXalf. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Evaluation of low-intensity pulsed ultrasound on doxorubicin delivery in 2D and 3D cancer cell cultures
<p>This data set includes raw data supporting the paper "<strong>Evaluation of low-intensity pulsed ultrasound on doxorubicin delivery in 2D and 3D cancer cell cultures </strong>".</p> <p><strong>The files include the following data</strong>:</p> <p>1. The raw data used for calculating <strong>doxorubicin penetration </strong>in <strong>2D</strong> cancer cells;</p> <p>2. The raw data used for calculating <strong>doxorubicin</strong> <strong>penetration </strong>into tumor spheroids (<strong>3D</strong> cultures).</p>
Raw data for the article: 3D Culture and Interferon-? Priming Modulates Characteristics of Mesenchymal Stromal/Stem Cells by Modifying the Expression of Both Intracellular and Exosomal microRNAs
<p>Mesenchymal stromal/stem cells (MSCs) have emerged as a therapeutic tool in regenerative medicine. Recent studies have shown that exosome (EXO)-derived microRNAs (miRNAs) play a crucial role in mediating MSC functions. Additionally, intracellular miRNAs have been found to regulate MSC therapeutic capacities. However, the molecular mechanisms underlying miRNA-mediated MSC effects are not fully understood. We used 3D culture and IFN-γ to prime/enhance the MSC therapeutic effects in terms of functional miRNAs. After priming, our analysis revealed stable variations in intracellular miRNA among the MSC biological replicates. Conversely, a significant variability of miRNA was observed among EXOs released from biological replicates of the priming treatment. For each priming, we observed distinct miRNA expression profiles between the MSCs and their EXOs. Moreover, in both types of priming, gene ontology (GO) analysis of deregulated miRNAs highlighted their involvement in tissue repair/regeneration pathways. In particular, the 3D culture enhanced angiogenic properties in both MSCs and EXOs, while IFN-γ treatment enriched miRNAs associated with immunomodulatory pathways. These findings suggest that 3D culture and IFN-γ treatment are promising strategies for enhancing the therapeutic potential of MSCs by modulating miRNA expression. Additionally, the identified miRNAs may contribute to understanding the molecular mechanisms underlying the miRNA-mediated therapeutic effects of MSCs.</p>
Global gene expression profiles of cardiac progenitors differentiated from human pluripotent stem cells in 3D culture under simulated microgravity
Efficient generation of cardiomyocytes from human pluripotent stem cells is critical for their regenerative applications. Microgravity and 3D culture can profoundly modulate cell proliferation and survival. Here we engineered microscale progenitor cardiac spheres from human pluripotent stem cells and exposed the spheres to simulated microgravity using a random positioning machine for 3 days during their differentiation to cardiomyocytes. Methods: RNA-seq libraries were prepared using the Illumina TruSeq RNA kit and the TrueSeq method was employed for mRNA enrichment. The libraries were quantified and samples were multiplexed in each lane of the flowcell. Cluster generation was performed and then sequenced on the Illumina HiSeq1000 system. Reads were mapped on the Human Genome Reference and normalized expression table was generated. Results: Among differentially expressed genes 53 of them were up-regulated and 75 were down-regulated. Conclusions: Data demonstrate increased expression of genes associated with growth development and pro-survival in cardiac progenitors cultured under simulated microgravity compared with those cultured under standard gravity. RNA-sequencing analysis was performed to compare global gene expression profiles of cells at differentiation day 8 under simulated microgravity vs. standard gravity.
Comparison of gene expression profiles of normal human bronchial epithelial cells in 2D and 3D cultural conditions
The experiment is part of a project to study DNA repair process after ionizing radiation in organotypic 3-dimentional human bronchial epithlial cell culture. Human bronchial epithelial cells were grown in tissue culture flask (2D) or in matrics gel (3D). Three independent cultures were done for each condition.
Impact of BMP and WNT signaling modulation on mesendoderm progenitor cells specification from hPSCs in 3D culture conditions
GEO Series GSE184302. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Global gene expression profiles of cardiac progenitors differentiated from human pluripotent stem cells in 3D culture under simulated microgravity
GEO Series GSE84582. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptional and functional analysis of human dopamine neurons in 3D fetal ventral midbrain organoid like cultures
GEO Series GSE192405. Homo sapiens. 13 samples. Type: Expression profiling by high throughput sequencing.
Comparison of gene expression profiles of normal human bronchial epithelial cells in 2D and 3D cultural conditions
GEO Series GSE27520. Homo sapiens. 6 samples. Type: Expression profiling by array.
Stochastic profiling of matrix-attached MCF10A-5E cells in 3D culture
GEO Series GSE120030. Homo sapiens. 32 samples. Type: Expression profiling by array.
Self-assembly of hybrid 3D cultures by integrating living and synthetic cells
GEO Series GSE308254. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
Reprogramming of dermal papilla cell intact gene signature with 3D culture and Lef-1 overexpression
GEO Series GSE121112. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
CloneSeq: A Highly Sensitive Single-cell Analysis Platform for Comprehensive Characterization of Cells from 3D Culture
GEO Series GSE155888. Homo sapiens; Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing.
RNA-sequencing of D2A1 and D2.OR cell lines in both 2D and 3D cultures
GEO Series GSE172882. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.