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5,412 results for “Cell differentiation”
Data from: Collagen vitrigel promotes hepatocytic differentiation of induced pluripotent stem cells into functional hepatocyte-like cells
Differentiation of stem cells to hepatocytes provides an unlimited supply of human hepatocytes and therefore has been vigorously studied. However, to date, the stem cell-derived hepatocytes were suggested to be of immature features. To obtain matured hepatocytes from stem cells, we tested the effect of culturing iPS cell-derived endoderm cells on collagen vitrigel membrane and compared with our previous reported nanofiber matrix. We cultured hiPS cell-derived endoderm cells on a collagen vitrigel membrane and examined the expression profiles, and tested the activity of metabolic enzymes. Gene expression profile analysis of hepatocytic differentiation markers revealed that upon culture on collagen vitrigel membrane, immature markers of AFP decreased, with a concomitant increase in the expression of mature hepatocyte transcription factors and mature hepatocyte markers such as ALB, ASGR1. Mature markers involved in liver functions, such as transporters, cytochrome P450 enzymes, phase II metabolic enzymes were also upregulated. We observed the upregulation of the liver markers for at least 2 weeks. Gene array profiling analysis revealed that hiPS cell-derived hepatocyte-like cells (hiPS-hep) resemble that of the primary hepatocytes. Functions of the CYP enzyme activities were tested in multi-institution and all revealed high CYP1A, CYP2C19, CYP2D6, CYP3A activity, which could be maintained for at least 2 weeks in culture. Taken together, the present approach identified that collagen vitrigel membrane provides a suitable environment for the generation of hepatocytes from hiPS cells that resemble many characteristics of primary human hepatocytes.
Dataset: ATML1 Regulates the Differentiation of ER Body-containing Large Pavement Cells in Rosette Leaves of Brassicaceae Plants
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raw data - circNR3C2 promote chondrogenic differentiation and cartilage repair of human adipose-derived stem cells via hsa-miR-647/SOX9 pathway
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Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation (Supplementary Tables)
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Figure 1 in Investigation the effects of vitreous humor on proliferation and dedifferentiation of differentiated NTERA2 cells
Figure 1. Cell count analysis of NT2, NT2-RA and NT2 RA-VH cells at 3 and 9 days after culturing at 6 well plates. NT2 RA-VH cell numbers were increased in comparison to those of the NT2-RA cells. Data represent the mean ± SEM. (a) P <0.05; (b) P <0.01 vs control group, compared with NT2-RA cells.
Figure 3 in Investigation the effects of vitreous humor on proliferation and dedifferentiation of differentiated NTERA2 cells
Figure 3. Flow cytometry analysis to assess the level of TRA-81, SSEA1, and SSEA3 cell surface antigens on NT2, NT2-RA, and NT2-RA cells treated with different concentrations of VH for 6 days. (A) NT2-RA cells treated with 2.5% and 7.5% VH; (B) NT2-RA cells treated with 15% VH.
Label-Free Differentiation of Living versus Dead Single Yeast Cells using Broadband Electrical Impedance Spectroscopy
<p>Data to support manuscript.</p>
Extending the gene regulatory network model for B cell differentiation
<p>Scripts used for modelling the gene regulatory network of B cell differentiation</p>
Tumour-intrinsic features shape T-cell differentiation through myeloma disease evolution - raw data
<p><strong><em>sample_id</em>.h5</strong></p> <ul> <li>Feature-barcode matrix (<em>filtered_feature_bc_matrix.h5</em>, 10x-Genomics-formatted hdf5 file) for indicated sample.</li> </ul> <p><strong><em>sample_id</em>-VDJ.csv</strong></p> <ul> <li><em>filtered_contig_annotations.csv</em> file for indicated sample.</li> </ul> <p><strong>sample-metadata.csv</strong></p> <ul> <li>Metadata for each sample: donor_id (donor of origin), sort (sorting strategy), batch (sequencing batch).</li> </ul> <p> </p>
TPP statistics data for: Plurifaceted proteomics method identifies a key regulator of translation during stem cells maintenance and differentiation
<p>Statistics data from TPP package.</p>
Data from: Phosphorylated Groucho delays differentiation in the follicle stem cell lineage by providing a molecular memory of EGFR signaling in the niche
In the epithelial follicle stem cells (FSCs) of the Drosophila ovary, Epidermal Growth Factor Receptor (EGFR) signaling promotes self-renewal, whereas Notch signaling promotes differentiation of the prefollicle cell (pFC) daughters. We have identified two proteins, Six4 and Groucho (Gro), that link the activity of these two pathways to regulate the earliest cell fate decision in the FSC lineage. Our data indicate that Six4 and Gro promote differentiation towards the polar cell fate by promoting Notch pathway activity. This activity of Gro is antagonized by EGFR signaling, which inhibits Gro-dependent repression via p-ERK mediated phosphorylation. We have found that the phosphorylated form of Gro persists in newly formed pFCs, which may delay differentiation and provide these cells with a temporary memory of the EGFR signal. Collectively, these findings demonstrate that phosphorylated Gro labels a transition state in the FSC lineage and describe the interplay between Notch and EGFR signaling that governs the differentiation processes during this period.
Image-derived models of cell organization changes during differentiation and drug treatments
PC12 cells are a popular model system to study changes driving and accompanying neuronal differentiation. While attention has been paid to changes in transcriptional regulation and protein signaling, much less is known about the changes in organization that accompany PC12 differentiation. Fluorescence microscopy can provide extensive information about these changes, although it is difficult to continuously observe changes over many days of differentiation. We describe a generative model of differentiation-associated changes in cell and nuclear shape and their relationship to mitochondrial distribution constructed from images of different cells at discrete time points. We show that the model accurately represents complex cell and nuclear shapes and learn a regression model that relates cell and nuclear shape to mitochondrial distribution; the predictive accuracy of the model increases during differentiation. Most importantly, we propose a method, based on cell matching and interpolation, to produce realistic simulations of the dynamics of cell differentiation from only static images. We also found that the distribution of cell shapes is hollow: most shapes are very different from the average shape. Finally, we show how the method can be used to model nuclear shape changes of human induced pluripotent stem cells resulting from drug treatments. [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text] [Media: see text]
Data from: Stem cell differentiation trajectories in Hydra resolved at single-cell resolution
The adult Hydra polyp continually renews all of its cells using three separate stem cell populations, but the genetic pathways enabling this homeostatic tissue maintenance are not well understood. We sequenced 24,985 Hydra single-cell transcriptomes and identified the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each cell lineage and identified gene modules and putative regulators expressed along these trajectories, thus creating a comprehensive molecular map of all developmental lineages in the adult animal. In addition, we built a gene expression map of the Hydra nervous system. Our work constitutes a resource for addressing questions regarding the evolution of metazoan developmental processes and nervous system function.
ChIP-seq - Definitive endoderm differentiation of human pluripotent stem cells in G1 phase
<p>Backup copy of the processed ChIP-seq data at http://ngs.sanger.ac.uk/production/endoderm/</p>
Confronting false discoveries in single-cell differential expression
<p>A repository containing 18 benchmarking datasets for single-cell method development.</p>
Microscopy data of RNA polymerase II clusters during RHB differentiation of cultured mouse embryonic stem cells
<p>Main repository containing the analysis scripts and results: 10.5281/zenodo.8013242</p>
Microscopy data of RNA polymerase II clusters during -LIF differentiation of cultured mouse embryonic stem cells
<p>Main repository containing the analysis scripts and results: 10.5281/zenodo.8013242</p>
INFLAMeR: a machine learning algorithm based on large-scale perturbation screening identified new lncRNAs regulating differentiation and survival of leukaemia cells
<p><strong>Abstract</strong></p> <p>Long non-coding RNAs (lncRNAs) are a diverse group of transcripts with poorly understood<br> functionality. To address this gap, we developed INFLAMeR, an advanced machine learning<br> model trained on CRISPRi screening data, to predict functional lncRNAs using comprehensive<br> genetic features. We experimentally validated the predictions by assessing their impact on cell<br> proliferation and anticancer drug resistance. Among the selected lncRNAs, 85% showed<br> significant effects upon knockdown, while low-scoring lncRNAs had no discernible impact.<br> Notably, our study elucidated the functional role of SNHG6 in hematopoietic differentiation.<br> INFLAMeR greatly enhances the prediction of functional lncRNAs, providing valuable insights<br> into their regulatory landscape. By integrating INFLAMeR with experimental validation, we can<br> identify and characterize functional lncRNAs in a cell-type-specific manner, contributing to a<br> deeper understanding of their involvement in cellular processes. Our findings revealed insights<br> into lncRNA biology and a framework for improving the identification of functional lncRNAs.</p>
Data from: Comparison of osteoclast differentiation protocols from human induced pluripotent stem cells of different tissue origins
<p class="MsoNormal"><span class="apple-converted-space"><span><strong>Background</strong>: </span></span><span class="apple-converted-space"><span>Ever since their discovery, induced pluripotent stem cells (iPSCs) have been extensively differentiated into a large variety of cell types. However, a limited amount of work has been dedicated to differentiating iPSCs into osteoclasts. </span></span><span>While several differentiation protocols have been published, it remains unclear which protocols or differentiation methods are preferable regarding the differentiation of osteoclasts.</span></p> <p class="MsoNormal"><span><strong>Methods</strong>: </span><span>In this study, we compare the osteoclastogenesis capacity of a peripheral blood mononuclear cell (PBMC)-derived iPSC line to a fibroblast-derived iPSC line in conjunction with either embryoid body-based or monolayer-based differentiation strategies. Both cell lines and differentiation protocols were investigated regarding their ability to generate osteoclasts and their inherent robustness and ease of use. The ability of both cell lines to remain undifferentiated while propagating using a feeder-free system was assessed using alkaline phosphatase staining. This was followed by evaluating mesodermal differentiation and the characterization of hematopoietic progenitor cells using flow cytometry. Finally, osteoclast yield and functionality based on resorptive activity, Cathepsin K, and tartrate-resistant acid phosphatase (TRAP) expression were assessed. Results were validated using qRT-PCR throughout the differentiation stages.</span></p> <p class="MsoNormal"><span><strong>Results</strong>: </span><span class="apple-converted-space"><span>Embryoid-body-based differentiation yielded CD45<sup>+</sup>, CD14<sup>+</sup>, and CD11b<sup>+</sup> subpopulations, which in turn differentiated into osteoclasts which demonstrated TRAP positivity, Cathepsin K expression, and mineral resorptive capabilities. This was regardless of which iPSC line was used. Monolayer-based differentiation yielded lower quantities of hematopoietic cells that were mostly CD34<sup>+</sup> and did not subsequently differentiate into osteoclasts.</span></span></p> <p class="MsoNormal"><span class="apple-converted-space"><span><strong>Conclusions</strong>: </span></span><span>The outcome of this study demonstrates the successful differentiation of osteoclasts from iPSCs in conjunction with the embryoid-based differentiation method, while the monolayer-based method did not yield osteoclasts. No differences were observed regarding osteoclast differentiation between the PBMC and fibroblast-derived iPSC lines.</span></p>
Testing the Addition of an Anti-cancer Drug, BAY 1895344, to Usual Chemotherapy for Advanced Stage Solid Tumors, With a Specific Focus on Patients With Small Cell Lung Cancer, Poorly Differentiated Ne
ClinicalTrials.gov study NCT04514497. IPD Sharing: YES. Countries: 1. Publications: 0.
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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.