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111,247 results for “cells”
Quantifying the Spatial Distribution of Fluorescently-Labeled Cell Markers in Stroma-Rich Tumors
<p>Cell measurements (intensity for various compartments, cell morphology, spatial distance from stroma) from image processing of mouse xenograft tumour tissues stained for DAPI, Pan Cytokeratin, Fibronectin, pNDRG1 or Ki67. </p>
Differential interference contrast (DIC) image of unstained living HepG2 human liver cancer cells
<p><strong>Introduction</strong></p> <p>This dataset is associated with our submission to Computers in Biology and Medicine, titled "Accurate Detection and Instance Segmentation of Unstained Living Adherent Cells in Differential Interference Contrast Images". The submission number for this manuscript is CIBM-D-23-09623R1.</p> <p><strong>Authors</strong>: Fei Pan, Yutong Wu, Kangning Cui, Shuxun Chen, Yanfang Li, Yaofang Liu, Adnan Shakoor, Han Zhao, Beijia Lu, Shaohua Zhi, Raymond Hon-Fu Chan, Dong Sun</p> <p><strong>Dataset Description</strong></p> <p>Our dataset comprises 520 differential interference contrast (DIC) images of 12,198 unstained HepG2 human liver cancer cells, each with a corresponding fluorescence image stained with calcein acetoxymethyl (AM), ensuring high-quality ground-truth annotations. Unique in addressing the multi-state nature of adherent cells commonly seen in wet labs, it includes both healthy and unhealthy cells in a single image, providing a valuable resource for studying multi-state cell detection and instance segmentation.<br>Citation</p> <p>We kindly request that researchers who use this dataset cite both our paper and this dataset. This will help acknowledge the work and facilitate further advancements in the field.</p> <p><br><strong>Please cite as follows:</strong></p> <p><strong>Paper:</strong><br>Pan, F., Wu, Y., Cui, K., Chen, S., Li, Y., Liu, Y., Shakoor, A., Zhao, H., Lu, B., Zhi, S., Chan, R. H.-F., & Sun, D. "Accurate detection and instance segmentation of unstained living adherent cells in differential interference contrast images,” <em>Computers in Biology and Medicine</em>, vol. 182, p. 109151, Nov. 2024, doi: 10/g5p9d8.</p> <p><strong>Dataset:</strong><br>Pan, F., Chen, S., Li, Y., Shakoor, A., Zhao, H., & Sun, D. (2024). Differential interference contrast (DIC) image of unstained living HepG2 human liver cancer cells. Zenodo. </p> <p>Thank you for your interest and support in our work. We look forward to seeing the innovative research that this dataset will enable.</p> <p> </p> <p> </p>
Western Blotting NSD3 in AML Cell Lines
<p>SGC Open Lab Notebook Project - Understanding the Role of NSD3 in Cancer </p> <p>Experiment 011 - Western blot of MOLM-13, UCSD-AML1, and HL-60 AML cell lines probing for NSD3. </p>
The sharing of research raw data in journals indexed in the Cell & Tissue Engineering JCR category (2011-2015)
<p>The availability of research data sets is an important milestone since it can enhance the dynamics of research. This study aims to analyze the PubMed Central repository to determine the availability and type of raw data sets in Cell & Tissue Engineering journals indexed in the Journal Citation Reports. The number and types of files were registered. A search of the 21 journals from the Cell & Tissue Engineering category of the 2015 Journal Citation Reports was conducted. Information was collected from October to December 2016. A study of the supplementary material of the original articles published between 2011-2015 was performed through a search in the PubMed Central repository, which is the most used free full-text repository in biomedicine. Only articles with supplementary material were retrieved. The number and types of files were registered. In cases where a compressed file, such as a .zip or .rar file, was found, it was opened to check what kinds of files it contained.</p>
Titration of ligands for the stimulation of MDA-MB-231 BRE and CAGA reporter cell lines
<p>Considerable amount of ligands will be consumed in the dual luciferase assay (DLA) which will be used for the screening of ALK2 inhibitors and off-target inhibition of ALK5 routinely. Ligands are costly to procure. In order to minimise wastage, it is important to determine the least amount of ligands needed to achieve optimal stimulation of ALK2 and ALK5. In these experiments, the activation of ALK2 and ALK5 by different concentrations of ligands in MDA-MB-231 reporter cells was analysed in Western Blot and DLA.</p>
Growth kinetics of the HSJD-DIPG-07 cell line in non-adherent culture
<p>The growth kinetics of the HSJD-DIPG-07 cell line when grown as neurospheres in non-adherent culture conditions.</p>
Mass spectra for single Scrippsiella trochoidea cells: light vs. dark & replete vs. N limiting conditions
<p>Data files for 77 <em>Scrippsiella trochoidea </em>cells measured in single cell MS experiments. Information about the experimental conditions, corresponding file names, the number of cells for which data are recorded in each respective file, and the range of acquisition times for individual cells can be found in the supplemental documentation of the corresponding manuscript titled : "Single Cell Metabolomic Analysis of <em>Scrippsiella trochoidea</em>" in Frontiers in Plant Science. </p> <p>Note: .mzML is a standard MS file format that can be viewed using freeware such as mMass (<a href="http://www.mmass.org/">http://www.mmass.org/</a>) and ProteoWizard (<a href="http://proteowizard.sourceforge.net/index.shtml">http://proteowizard.sourceforge.net/index.shtml</a>).</p> <p> </p> <p> </p> <p> </p>
Determining the transfectability of different patient-derived cell lines
<p>Determining whether the following patient-derived cell lines can be transfected efficiently using Lipofectamine 2000</p> <p>C2C12</p> <p>HSJD-DIPG-008</p> <p>HSJD-DIPG-011</p> <p>HSJD-DIPG-012</p> <p>HSJD-DIPG-013</p> <p>SU-DIPG-IV</p> <p>HSJD-GBM-002</p> <p>HSJD-DIPG-007</p> <p> </p>
Efficacy of inhibitor on wild-type ACVR1 and R206H mutant in C2C12 cells (by DLA)
<p>There are concerns that compounds that are effective in inhibiting ALK2 by occupying its ATP-binding pocket might have reduced efficacy against mutant ALK2. That will be undesirable since the compounds should also target the mutant gain-of-function ALK2 in DIPG cells. The following experiment takes advantage of the fact that ALK2-R206H mutant confers a neofunction of being activated by Activin A (not activating towards wild-type ALK2). Therefore, using Activin A as the stimulation ligand, the effectiveness of inhibition on ALK2-R206H can be specifically determined. BMP6 which activates both wild-type ALK2 and ALK2-R206H is also included.</p>
Experimental data used in the manuscript (Jagiella et al., Cell Systems, 4(2), 2017)
<p>This folder contains raw and processed data used in the manuscript:</p> <p>Jagiella, N. and Rickert, D. and Theis, F. J. and Hasenauer, J. (2017). Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models. Cell Systems, 4(2):194-206.</p>
Microscopy images and movies supporting the publication: "tRNA tracking for direct measurements of protein synthesis kinetics in live cells"
<p>This repository contains experimental and simulated microscopy movies and images supporting the publication: Volkov et al. (2018) tRNA tracking for direct measurements of protein synthesis kinetics in live cells. <em>Nat Chem Biol, </em>DOI: 10.1038/s41589-018-0063-y</p> <p>A detailed list of files and file organisation can be found in Repository_content.pdf.</p>
Huntingtin nanobody purification using osmotic shock cell lysis and growth in M9 media – 2018/04/09
<p>Huntingtin structure-function open lab notebook project. Huntingtin nanobody purification using osmotic shock cell lysis and growth in M9 media – 2018/04/09</p>
Huntingtin nanobody purification using osmotic shock cell lysis – 2018/04/02
<p>Huntingtin structure-function open lab notebook project. Huntingtin nanobody purification using osmotic shock cell lysis – 2018/04/02.</p>
Constriction rate modulation can drive cell size control and homeostasis in C. crescentus. Data part 2.
<p>This data corresponds to the publication "Constriction rate modulation can drive cell size control and homeostasis in <em>C. crescentus</em>".</p> <p>This is part 2 out of 2.</p> <p>Part 1: 10.5281/zenodo.1172042</p> <p>See metadata.docx for more information.</p>
Dataset for "Role of electron-phonon coupling and thermal expansion on band gaps, carrier mobility, and interfacial offsets in kesterite thin-film solar cells"
<p>Dataset for "Role of electron-phonon coupling and thermal expansion on band gaps, carrier mobility, and interfacial offsets in kesterite thin-film solar cells"</p>
Small scale test-expression of full-length huntingtin Q23 with HAP40 in baculoviral expression system production in sf9 insect cells – 2018/05/14
<p><strong>Project</strong> - Huntingtin structure-function open lab notebook. </p> <p><strong>Experiment and rationale</strong> - Small scale test-expression of full-length huntingtin Q23 with HAP40 in baculoviral expression system production in sf9 insect cells – 2018/05/14. To validate our insect cell production system for the generation of physiologically relevant huntingtin constructs, HTT and HAP40 will be co-expressed and purified from sf9 culture. </p>
Constriction rate modulation can drive cell size control and homeostasis in C. crescentus. Data part 1.
<p>This data corresponds to the publication "Constriction rate modulation can drive cell size control and homeostasis in <em>C. crescentus</em>".</p> <p>This is part 1 out of 2.</p> <p>Part 2: 10.5281/zenodo.1241005 </p> <p>See metadata.docx for more information.</p>
Large scale expression and purification of full-length huntingtin Q23 with and without HAP40 from baculoviral expression system production in sf9 insect cells – 2018/06/04
<p><strong>Project</strong> - Huntingtin structure-function open lab notebook. </p> <p><strong>Experiment and rationale</strong> - Purified huntingtin samples with and without stabilising binding partners (e.g. HAP40) are required for use in structural and functional studies, in particular SAXS experiments. </p>
Large scale expression and purification of full-length huntingtin Q23 with HAP40 from baculoviral expression system production in sf9 insect cells – 2018/05/28
<p><strong>Project</strong> - Huntingtin structure-function open lab notebook. </p> <p><strong>Experiment and rationale</strong> - Purified huntingtin samples with stabilising binding partners (e.g. HAP40) are required for use in structural and functional studies, in particular SAXS experiments. </p>
Single-particle tracking data for "CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning"
<p>This dataset contains all the raw SPT data reported in "­­­­CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning" in the form of SPT trajectories. The SPT trajectories are provided in two different formats for convenience: a CSV format and a Matlab format. Both formats are readable by Spot-On: https://spoton.berkeley.edu/</p> <p>The SPT data contains "fast tracking" spaSPT data and this data was analyzed using the Matlab version of Spot-On which can be found and downloaded at: https://gitlab.com/tjian-darzacq-lab/spot-on-matlab</p> <p> </p> <p>Full details about the Matlab and CSV formats are provided in the ReadMe files in the associated zip files.</p> <p>Please see the associated manuscript for a detailed description of how the data was acquired and analyzed.</p>
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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.