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The raw data of the genome-wide CRISPR screens for VHL-WT and VHL-L188V Kelly cells

The raw data including the conditions, reference, and PoolQ output files of the genome-wide CRISPR screens for VHL-WT and VHL-L188V Kelly cells were published in the paper "Total loss of VHL gene function impairs neuroendocrine cancer cell fitness due to excessive HIF2α activity".

opencc-by-4.0Aug 2024View details →

Comparison of Fixed Single Cell RNA-seq Methods to Enable Transcriptome Profiling of Neutrophils in Clinical Samples - Time course data

Monitoring neutrophil gene expression is a powerful tool for understanding disease mechanisms, developing new diagnostics, therapies and optimizing clinical trials. Neutrophils are sensitive to the processing, storage and transportation steps that are involved in clinical sample analysis. This study is the first to evaluate the capabilities of technologies from 10X Genomics, PARSE Biosciences, and HIVE (Honeycomb Biotechnologies) to generate high-quality RNA data from human blood-derived neutrophils. Our comparative analysis shows that all methods produced high quality data, importantly capturing the transcriptomes of neutrophils. 10X FLEX cell populations in particular showed a close concordance with the flow cytometry data. Here, we establish a reliable single-cell RNA sequencing workflow for neutrophils in clinical trials: we offer guidelines on sample collection to preserve RNA quality and demonstrate how each method performs in capturing sensitive cell populations in clinical practice. This dataset includes only the 10X Flex time course data and analysis.

Genetic instruments for blood cell traits

This dataset includes summary statistics for genetic instruments for 9 blood cell trait phenotypes. These genetic instruments were developed in the UK Biobank and were used in several Mendelian randomization studies, including an analysis of childhood acute lymphoblastic leukemia (Kachuri et al. 2021; PMID 34469753) and glioma subtypes (Kachuri et al. 2024). Details of the GWAS and instrument development process are described in: https://pubmed.ncbi.nlm.nih.gov/34469753/

Supplementary files for "Tristetraprolin Affects Invasion-Associated Genes Expression and Cell Motility in Triple-Negative Breast Cancer Model"

Track1 and Track3 - raw numerical data on cell tracking; Morphology-DXR treated - raw images of the cells, treated with DXR; Morphology ecTTP+WT - morphology of wild-type and TTP-overexpressing cells; RAW data qPCR - rew data of gene expression experiments

Figure 8 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol

Figure 8. Treatment Group with resveratrol tempeh + 2-ME after induced by Beta-Amyloid (10 x10).

Figure 5 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol

Figure 5. Treatment group: 2- ME (10 x10).

Figure 9. Treatment Group with 2 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol

Figure 9. Treatment Group with 2-ME after induced by Beta-Amyloid (10 x10).

Figure 2 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol

Figure 2. Treatment group: 2- ME + Resveratrol Standard (10 x10).

Figure 1 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol

Figure 1. Control Group (10 x10).

Table 4 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol

Table 4. Cytotoxic effect of various concentrations of Resveratrol and 2-Methoxyethanol Against Primary Neuron cell viability in MTT assay (570 nm).<table><tbody><tr><th>% Inhibition</th></tr></tbody><tbody><tr><th>Concentration of 2-Methoxyethanol</th><td>2-ME (10mM)</td><td>2-ME (10mM)</td><td>2-ME (10mM)</td></tr><tr><th>and Resveratrol</th><td>Resveratrol (Standard)</td><td>Resveratrol (Tempeh)</td><td>Resveratrol (Soybean Seed Coat)</td></tr><tr><th>IC50</th><td>(17.38 ± 0.99 µg/mL)</td><td>(31.14 ± 0.02 µg/mL)</td><td>(13.40 ± 0.30 µg/mL)</td></tr><tr><th>1.4 (µg/mL)</th><td>12.57</td><td>0</td><td>11.98</td></tr><tr><th>2.8 (µg/mL)</th><td>4.59</td><td>1.75</td><td>17.03</td></tr><tr><th>4.2 (µg/mL)</th><td>0</td><td>0</td><td>0</td></tr></tbody></table>

Table 3 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol

Table 3. Cytotoxic effect of various concentrations of Resveratrol and 2-Methoxyethanol Against Primary Neuron cell viability in MTT assay (540 nm).<table><tbody><tr><th>% Inhibition</th></tr></tbody><tbody><tr><th>Concentration of 2-Methoxyethanol</th><td>2-ME (10mM)</td><td>2-ME (10mM)</td><td>2-ME (10mM)</td></tr><tr><th>and Resveratrol</th><td>Resveratrol (Standard)</td><td>Resveratrol (Tempeh)</td><td>Resveratrol (Soybean Seed Coat)</td></tr><tr><th>IC50</th><td>(17.64 ± 0.99 µg/mL)</td><td>(32.22 ± 1.18 µg/mL)</td><td>(17.43 ± 0.16 µg/mL)</td></tr><tr><th>1.4 (µg/mL)</th><td>11.8</td><td>0</td><td>7.95</td></tr><tr><th>2.8 (µg/mL)</th><td>5.27</td><td>0</td><td>14.41</td></tr><tr><th>4.2 (µg/mL)</th><td>0</td><td>0</td><td>0</td></tr></tbody></table>

Supporting Data for "Why Half‐Cell Samples Provide Limited Insight Into the Aging Mechanisms of Potassium Batteries"

This dataset provides the raw data to the manuscript "Why Half‐Cell Samples Provide Limited Insight Into the Aging Mechanisms of Potassium Batteries" published in Advanced Energy Materials, 2024, DOI 10.1002/aenm.202403811 <a href="https://doi.org/10.1002/aenm.202403811">Link to Publisher</a>   Comments: <ul> <li>HAXPES synchrotron data is provided as IGOR file (IGOR Pro (v6.37, WaveMaterics Inc.). The file contains the original 2D data and the converted 1D datasets used for analysis</li> <li>In-House XPS data is provided with corresponding peak fits as excel spreadsheet</li> <li>peak data (binding energy (after referencing), intensity, area, FWHM and at.%) is provided in separate excel spreadsheet.</li> </ul>

opencc-by-4.0Aug 2024View details →

Supporting information and Figures of the article "Harnessing the Biomimetic Effect of Macromolecular Crowding in the Cell-Derived Model of Clubfoot Fibrosis"

Open the record for dataset details and reuse information.

Table 2 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol

Table 2. Effect of Various concentrations of Resveratrol and 2-Methoxyethanol against Primary Neuron cell viability (570 nm).<table><tbody><tr><th>% Cell Viability</th></tr></tbody><tbody><tr><th>Concentration of 2-Methoxyethanol</th><td>2-ME (10mM)</td><td>2-ME (10mM)</td><td>2-ME (10mM)</td></tr><tr><th>and Resveratrol</th><td>Resveratrol (Standard)</td><td>Resveratrol (Tempeh)</td><td>Resveratrol (Soybean Seed Coat)</td></tr><tr><th>1.4 (µg/mL)</th><td>87.43</td><td>100</td><td>88.02</td></tr><tr><th>2.8 (µg/mL)</th><td>95.41</td><td>98.25</td><td>82.97</td></tr><tr><th>4.2 (µg/mL)</th><td>100</td><td>100</td><td>100</td></tr></tbody></table>

Table 1 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol

Table 1. Effect of Various concentrations of Resveratrol and 2-Methoxyethanol against Primary Neuron cell viability (540 nm).<table><tbody><tr><th>% Cell Viability</th></tr></tbody><tbody><tr><th>Concentration of 2-Methoxyethanol</th><td>2-ME (10mM)</td><td>2-ME (10mM)</td><td>2-ME (10mM)</td></tr><tr><th>and Resveratrol</th><td>Resveratrol (Standard)</td><td>Resveratrol (Tempeh)</td><td>Resveratrol (Soybean Seed Coat)</td></tr><tr><th>1.4 (µg/mL)</th><td>88.2</td><td>100</td><td>92.05</td></tr><tr><th>2.8 (µg/mL)</th><td>94.73</td><td>100</td><td>85.59</td></tr><tr><th>4.2 (µg/mL)</th><td>100</td><td>100</td><td>100</td></tr></tbody></table>

opencc-by-4.0Aug 2024View details →

Single-cell datasets for Spherical Manifolds Capture Drug-Induced Changes in Tumor Cell Cycle Behavior

Single-cell dataset for Spherical Manifolds Capture Drug-Induced Changes in Tumor Cell Cycle Behavior by Wen et al. This is a single-cell T47D ER+/HER2- cancer dataset, where rows are individual cells, and columns are proteomic features measured using iterative immunofluorescent imaging (4i). Cell cycle phase annotations are found in the 'phase' column, and the 'Metadata_well' column refers to nanomolar treatment doses of palbociclib, from an untreated population (0 nM), up to 1,000 nM. Data are z-normalized across all treatment conditions. Please refer to the manuscript for full experimental details.

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

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, Journal of Advanced Research, Volume 62, 2024, Pages 119-141, ISSN 2090-1232, https://doi.org/10.1016/j.jare.2023.09.041.

Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function

Dataset for Ono et al., 2024. Contains all source data from the Tarchini laboratory, including illustrative images and raw data for quantification, as well as the data file containing statistical analysis. It also contains the data file produced by the Cullen laboratory reporting behavioral data.

opencc-by-4.0May 2024View details →

Studying gastrulation by invagination: the bending of a cell sheet by mechanical cell properties using 3D deformable cell based simulations

This dataset contains the scripts and end results of invagination simulation experiments. The data are the results of a 3D cell based model that was used to investigate invagination: the bending of a cell sheet, and uses cell-cell adhesion, apical constriction, cell volume conservation, collision detection and handeling.