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5,412 results for “Cell differentiation”
Efficient improvement of the proliferation, differentiation, and anti-arthritic capacity of mesenchymal stem cells by simply culturing on the immobilized FGF2 derived peptide, 44-ERGVVSIKGV-53
<p>All data needed to evaluate the results presented in the paper: Soo Bin Lee, Ahmed Abdal Dayem, Sebastian Kmiecik, Kyung Min Lim, Dong Sik Seo, Hyeong-Taek Kim, Polash Kumar Biswas, Minjae Do, Deok-Ho Kim, Ssang-Goo Cho, Efficient improvement of the proliferation, differentiation, and anti-arthritic capacity of mesenchymal stem cells by simply culturing on the immobilized FGF2 derived peptide, 44-ERGVVSIKGV-53,<br>Journal of Advanced Research, Volume 62,<br>2024,<br>Pages 119-141,<br>ISSN 2090-1232,<br>https://doi.org/10.1016/j.jare.2023.09.041.</p>
Amacrine cells differentially balance zebrafish colour circuits in the central and peripheral retina
<p>In vertebrate vision, the feature-extracting circuits of the inner retina are driven by photoreceptors whose outputs are already pre-processed. In zebrafish, for example, outer retinal circuits split "colour" from "greyscale" information across all four cone-photoreceptor types. How does the inner retina process this incoming spectral information while also combining cone signals to shape new greyscale functions?</p> <p>We address this question by imaging the light-driven responses of amacrine cells (ACs) and bipolar cells (BCs) in larval zebrafish, in the presence and pharmacological absence of inner retinal inhibition. We find that amacrine cells exert distinct effects on greyscale processing depending on retinal region, as well as contributing to the generation of colour opponency in the central retina. However, in the peripheral retina amacrine cells enhanced opponency in some bipolar cells while at the same time suppressing pre-existing opponency in others, such that the net change in the number of colour-opponent units was essentially zero. To achieve this 'dynamic balance' ACs counteracted intrinsic colour opponency of BCs via the On-channel. Consistent with these observations, Off-stratifying ACs were exclusively achromatic, while all colour opponent ACs stratified in the On-sublamina.</p> <p>This study reveals that the central and peripheral retina of larval zebrafish employ fundamentally distinct inhibitory circuits to control the interaction between greyscale- and colour-processing. Differential actions on the On- and Off-channels control the transmission of colour-opponent signals in the periphery.</p>
Single-cell RNA-seq count data used in differential expression benchmark study
<p>Count matrices and meta data tables from simulated and real world immune cell single-cell RNA-seq experiments.</p> <p>All files are in Rds format and can be read by R using "readRDS()". </p> <ul> <li>10k_*: These files contain a filtered version of the 10k Human PBMCs, 3' v3.1 data <a href="https://www.10xgenomics.com/resources/datasets/10k-human-pbmcs-3-v3-1-chromium-controller-3-1-high">published</a> by 10x Genomics</li> <li>blueprint_data.Rds: This file contains the bulk RNA-seq data downloaded from <a href="http://dcc.blueprint-epigenome.eu">BLUEPRINT</a></li> <li>blueprint_immune_comparisons.Rds: Results from running three bulk RNA-seq differential expression methods</li> <li>sim_data*: These files contain the count matrices and meta data tables for the simulated data. Every file contains a list of 13 replicates.</li> </ul> <p> </p>
Extended Data for Single-cell Transcriptional Uncertainty Landscape of Cell Differentiation
<p>The dataset includes supporting information for the study titled "Single-cell Transcriptional Uncertainty Landscape of Cell Differentiation".</p>
Lattice kinetic Monte Carlo model to simulate RNA polymerase II clusters during stem cell differentiation
<p>This data set includes Python scripts (numerical simulation and analysis) and already generated simulation data for RNA polymerase II clusters during stem cell differentiation. It includes the whole data to recreate panels.</p>
Microscopy-based assessment of RNA polymerase II clusters during differentiation of cultured mouse embryonic stem cells
<p>This repository contains the data and MatLab analysis scripts of the analysis of RNA polymerase II clusters over the course of differentiation of cultured mouse embryonic stem cells (mESCs). The cells were induced towards differentiation by either withdrawal of lineage-inhibiting factors (-LIF) or by RHB treatment. Both treatments were carried out in duplicate in independent experiments. Time course data were obtained by collection of cells at 3, 6, 12, 24, and 48 hours following the beginning of induction. Control data from unindexed cells were obtained at 24 and 48 hours. Cells were cultured, treated, collected, and fixed at University Medical Center Göttingen by Yomna Gohar, Priya Kumar, and Carmelo Ferrai. Fixed cells were fluorescently labeled and microscopy images were recorded and analyzed at Karlsruhe Institute of Technology by Lennart Hilbert. </p> <p>To analyse date data, the raw image data are first extracted into MatLab-native files using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/MultiPosition_extraction_nd2.m">MultiPosition_extraction_nd2.m</a> script. The actual analysis is then carried out using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ClusterAnalysis.m">ClusterAnalysis.m</a> script. Example microscopy images were produced using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ExampleImages.m">ExampleImages.m</a> script. The extracted data can be reviewed using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ReviewExtractedStacks.m">ReviewExtractedStacks.m</a> script.</p> <p>This is the main repository, containing the image analysis scripts alongside the links to the raw image data used in the analysis. The raw data are too large to be stored within this single repository, and therefore can be found at the following additional addresses.</p> <p>Differentiation by withdrawal of lineage-inhibiting factors (-LIF): <a href="https://doi.org/10.5281/zenodo.8013281">10.5281/zenodo.8013281</a></p> <p>Differentiation with addition of RHB for neuronal fate induction (RHB): <a href="https://doi.org/10.5281/zenodo.8013307">10.5281/zenodo.8013307</a></p>
Data from: Hemin treatment drives viral reactivation and plasma cell differentiation of EBV latently infected B cells
<p>Epstein-Barr virus (EBV) and <em>Plasmodium falciparum</em> have a well described role in the development of endemic Burkitt lymphoma (BL), yet the mechanisms involved remain unknown. A major hallmark of malarial disease is hemolysis and bystander eryptosis of red blood cells, which causes release of free heme in large quantities into peripheral blood. We hypothesized that heme released during malaria infection drives differentiation of latently infected EBV-positive B cells, resulting in viral reactivation and release of infectious virus. To test this hypothesis, we used the EBV-positive Mutu I B-cell line and treated with hemin (the oxidized form of heme) and evaluated for evidence of EBV reactivation. Hemin treatment resulted in the expression of EBV immediate early, early and late lytic gene transcripts. In addition, expression of CD138, a marker of plasma cells was co-expressed with the late lytic protein gp350 on hemin treated Mutu I cells. Finally, DNase-resistant EBV DNA indicative of virion production was detected in supernatant. To assess the transcriptional changes induced by hemin treatment, RNA sequencing was performed on mock- and hemin-treated Mutu I cells, and a shift from mature B cell transcripts to plasma cell transcripts was identified. To identify the mechanism of hemin-induced B cell differentiation, we measured levels of the plasma cell transcriptional repressor, BACH2, that contains specific heme binding sites. Hemin treatment caused significant degradation of BACH2 by 24 hours post-treatment in four BL cell lines (two EBV positive, two EBV negative). Knockdown of BACH2 in Mutu I cells using siRNAs significantly increased CD138+gp350+ cells to levels similar to treatment with hemin. This suggested that hemin induced BACH2 degradation was responsible for plasma cell differentiation and viral reactivation. Together, these data support a model where EBV reactivation can occur during malaria infection via heme modulation, providing a mechanistic link between malaria and EBV. </p>
Cluster of Differentiation Antigen 19/22(CD19/22) CAR T Cells (AUTO3) for the Treatment of Diffuse Large B Cell Lymphoma
ClinicalTrials.gov study NCT03287817. IPD Sharing: Not stated. Countries: 2. Publications: 2.
Beta Cell Function in Type 2 Diabetes: Differential Effects of SGLT2 Inhibitors and GLIP-Receptor Agonists
ClinicalTrials.gov study NCT07325435. IPD Sharing: NO. Countries: 1. Publications: 11.
RAD001 With Paclitaxel and Carboplatin in First Line Treatment of Patients With Advanced Large Cell Lung Cancer With Neuroendocrine Differentiation
ClinicalTrials.gov study NCT01317615. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Sox2 interacts with Atoh1 and Huwe1 loci to regulate Atoh1 transcription and stability during hair cell differentiation
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Data from: Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug
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Single cell multiomic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients
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CD8+ T cell differentiation status correlates with the feasibility of sustained unresponsiveness following oral immunotherapy
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Data from: Hemin treatment drives viral reactivation and plasma cell differentiation of EBV latently infected B cells
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Data for: Rigidity sensing of inclusions directs differentiated cell elongation and force generation across phenotypes
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Data from: Drosophila medulla neuroblast termination via apoptosis, differentiation and gliogenic switch is scheduled by the depletion of the neuroepithelial stem cell pool
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Data from: Fibroblasts modulate epithelial cell behavior within the proliferative niche and differentiated cell zone within a human colonic crypt model
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Amacrine cells differentially balance zebrafish colour circuits in the central and peripheral retina
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Antigen-specific CD4+ T cells promote monocyte recruitment and differentiation into glycolytic lung macrophages to control Mycobacterium tuberculosis
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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.