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7,157 results for “Cell lines”
A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing
<p>This is a public repository containing secondary datasets described in the publication <a href="https://doi.org/10.26508/lsa.202302481">"A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing"</a>. Primary data for this project are available at NCBI/SRA under the BioProject accession numbers PRJNA600820 and PRJNA834955, and include the following sequencing datasets:</p> <p>REH cell line:</p> <ul> <li>PacBio WGS</li> <li>ONT Ultralong WGS</li> <li>Illumina short-read PCR-free WGS</li> <li>IsoSeq RNA-seq</li> <li>Illumina short-read RNA-seq</li> </ul> <p>GM12878 cell line:</p> <ul> <li>Illumina short-read RNA-seq</li> </ul> <p>This dataset includes the following files:</p> <p><strong>Depth of Coverage analysis</strong></p> <ul> <li>Output from `samtools coverage`: <em>samtools.coverage.illumina.txt, samtools.coverage.ont.txt, samtools.coverage.pb.txt</em></li> <li>Output from `copycat` (binned coverage): <em>copycat.ont.coverage.10kb.csv, copycat.pb.coverage.10kb.csv, copycat.pcrfree.coverage.10kb.csv</em></li> </ul> <p><strong>Structural Variant (SV) callsets</strong></p> <ul> <li><strong>Raw:</strong> <em>illumina.tiddit.vcf, ont.sniffles.vcf, pb.sniffles.vcf</em></li> <li><strong>Filtered: </strong><em>REH.svs.filtered.csv</em></li> </ul> <p><strong>SNV callsets</strong></p> <ul> <li><strong>Filtered and annotated:</strong> <em>REH.mutect.filtered.ann.vcf.gz</em></li> </ul> <p><strong>Fusion gene callsets</strong></p> <ul> <li><strong>Short-read: </strong><em>GM12878.fusionreport.txt, illumina.all.txt, illumina.filtered.csv, REH.arriba.fusions.tsv, REH.fusioncatcher.fusion-genes.txt, REH.pizzly.txt, REH.squid.fusions.annotated.txt, REH.starfusion.abridged.tsv, REH.pdf</em></li> <li><strong>Long-read: </strong><em>cupcake.long.csv, cupcake.std.csv, jaffa_results.csv</em></li> <li><strong>Filtered: </strong><em>REH.fusions.filtered.csv</em><br> </li> </ul> <p> </p>
Isosceles paper simulated ovarian cell line ONT data (bulk RNA-Seq)
<div> <p>Simulated ovarian cell line ONT data (bulk RNA-Seq) for the Isosceles paper - more details can be found in the <a href="https://github.com/Genentech/Isosceles_Paper" target="_blank" rel="noopener">Isosceles_Paper</a> repository.</p> </div>
miRNA profiling of human nasopharyngeal carcinoma cell lines HONE1 and CNE2 after X-ray therapy
<p>The package contains two file:</p> <p>Supplementary Table 1. Kruskal Wallis test for cell viability rate</p> <p>Supplementary Table 2. Kruskal Wallis test for apoptosis rate</p> <p>The HONE1 and CNE2 cells were irradiated with X-rays at doses of 4 Gy, 8 Gy, 16 Gy and 20 Gy for 24 h. The cell viability rate and apoptosis rate were compared.</p>
An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line
<p>In this protocol, we describe the 4C-seq method in detail using RAW264.7 cells, a mouse macrophage cell line widely used to study acute and metabolic inflammation. We specifically outline how cistrome and epigenome data can be integrated into the primer designing step, critical for the entire protocol. Because intra-TAD chromatin loops are facilitated by transcription factors and coregulators, many of which are co-localized in open chromatin regions, the binding centers of those factors can be obtained by chromatin immunoprecipitation sequencing (ChIP-seq). The binding sites of these factors reflect the coherent loci of the chromatin loops and therefore can be used as references to improve the accuracy of the 4C primers. We specifically describe the 4C protocol using examples of recently identified Ccl2 enhancer and silencer as bait. <br> </p>
Investigation the cytotoxicity of newly synthesized quinazo-line–sulfonamide derivatives in human leukemia cell lines and hematopoietic activity in zebrafish embryos.
<p>These videos contain the time lapse imaging of the wild type zebrafish embryos showing the circulation, control (mock 0.5% V/V DMSO) and compound 4a treated embryos at 72 hours post fertilization. The compound 4a specifically blocked the formation of blood and no circulation was seen in these embryos. </p>
TALON output for WTC11 cell lines
<p>A range of long-read RNA-seq protocols is analyzed with TALON from WTC11 for the LRGASP challenge. We deposit our results here for further analysis. </p>
The effect of antidepressants on genes of endoplasmic reticulum stress in human astrocyte cell line.
<p>Many central nervous system (CNS) diseases, including major depressive disorder (MDD), are underpinned by the unfolded protein response (UPR) activated under endoplasmic reticulum (ER) stress. New, more efficient, therapeutic options for MDD are needed to avoid adverse effects and drug resistance. Therefore, the aim of the work was to determine whether UPR signalling pathway activation in astrocytes may serve as a novel target for antidepressant drugs. Among the tested antidepressants (escitalopram, amitriptyline, S-ketamine), only S-ketamine induced the expression of most ER stress-responsive genes in astrocytes.</p> <p><a href="https://doi.org/10.3390/pharmaceutics14040846">https://doi.org/10.3390/pharmaceutics14040846</a></p> <p> </p>
Constructing Lentiviral NSD3-Short-3xFLAG Constructs to Transduce AML Cell Lines
<p>SGC Open Lab Notebook Project - Understanding the Role of NSD3 in Cancer </p> <p>Funding Acknowledgment: The SGC is a registered charity (number 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada through Ontario Genomics Institute [OGI-055], Innovative Medicines Initiative (EU/EFPIA) [ULTRA-DD grant no. 115766], Janssen, Merck KGaA, Darmstadt, Germany, MSD, Novartis Pharma AG, Ontario Ministry of Research, Innovation and Science (MRIS), Pfizer, São Paulo Research Foundation-FAPESP, Takeda, and Wellcome.</p>
FLAIR2 results from LRGASP R2C2 sequencing of Human WTC11 and Mouse ES cell lines
<p>FLAIR2 results from Oxford Nanopore sequencing of R2C2 libraries generated from Human WTC11 and Mouse ES cell lines from the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) (Pardo-Palacios et al. Nature Methods 2024). FLAIR2 high-confidence isoforms are provided for WTC11 and ES cells. For Mouse ES cells, sequence variants were identified with Longshot and incorporated into transcript isoforms using FLAIR2. These data are associated with the FLAIR2 publication (Tang et al. 2024)</p>
Fluorescent images of actin and DAPI-labelled MCF10A, MCF7 and MDA-MB-231 cell lines
<p>This dataset of cell images was generated to understand the morphological changes between less and more metastic cancer cells and between normal and cancerous cells. They have been used in the linked publications.</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>
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>
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>
Optimisation of viability assay for DIPG patient-derived cell lines
<p>Evaluation of the efficacy of M4K compounds in DIPG patient-derived cell lines is essential before any promising compounds can be further tested in mouse xenograft models. This approach can aid in narrowing down clinical compound candidates and reduce the time, resources and animal sacrifice needed downstream.</p> <p>A robust and efficient readout for the changes in the viability of the DIPG cells needs to be established before it can be used to evaluate the M4K compounds. In addition, the amount of cells to be seeded at the beginning of the experiment has to be optimised to avoid overcrowding and starvation of the cells after extended culture times. Overcrowding and starvation will lead to increased cell death and prevent accurate estimation of the potency of M4K compounds (EC50).</p>
Different methods to evaluate the effects of M4K compounds on DIPG patient-derived cell lines
<p>Aside from determining the optimal numbers of DIPG cells to be seeded for viability assay, it is also important to validate that measurements using CellTiter Glo are in agreement with other methods of determining cell viability.</p> <p>For my blog post about this experiment, please visit my opennotebook page.</p> <p>https://openlabnotebooks.org/different-methods-to-evaluate-the-effects-of-m4k-compounds-on-dipg-patient-derived-cell-lines/</p>
A bioactive compound isolated from Duku (Lansium domesticum Corr) fruit peels exhibits cytotoxicity against T47D cell line
<p><strong>Background: </strong>Breast cancer is a major health problem for women globally. Many attempts have been promoted to cure cancer by finding new anticancer medicines from natural resources. Despite the richness of biodiversity discovered, there are some natural resources that remain unexplored. Fruit peels of Duku (<em>Lansium domesticum</em> Corr.) are rich with compounds that may have the potential to be developed as anticancer drugs. This study aimed to isolate cytotoxic compounds from the fruit peels of <em>L. domesticum</em> and assess their cytotoxic nature against T47D cells.</p> <p><strong>Methods: </strong>Powdered peels were macerated with ethyl acetate and the filtrate was evaporated to give EtOAc extract A. Dried extract A was triturated with n-hexane to give n-hexane soluble fraction B and insoluble fraction C. The cytotoxic nature of these three samples were assessed using MTT assay using T47D cells and doxorubicin as a control</p> <p><strong>Results: </strong>Fraction C that showed the smallest IC<sub>50</sub> (25.56 + 0.64µg/mL) value compared to extract A and fraction BFraction C was further fractionated by vacuum liquid chromatography to give 6 subfractions. Subfraction 2 showed a single compound based on thin layer chromatography, and this compound was identified as Lamesticumin A on the basis of its spectroscopic data. Lamesticumin A demonstrated cytotoxic activity against T47D cell lines with an IC<sub>50</sub> value of 15.68 + 0.30µg/mL.</p>
Figure 2 in Explore the antiproliferative phytocompounds from ethanolic extracts of Citrus paradisi against liver cancer cell line by chemical analysis using TLC and FT-IR spectroscopy
Figure 2. Anti-proliferative activity of ethanolic Citrus paradisi leaves extract.
Figure 3 in Explore the antiproliferative phytocompounds from ethanolic extracts of Citrus paradisi against liver cancer cell line by chemical analysis using TLC and FT-IR spectroscopy
Figure 3. FTIR analysis of ethanolic Citrus paradisi fruits extract.
Figure 1 in Explore the antiproliferative phytocompounds from ethanolic extracts of Citrus paradisi against liver cancer cell line by chemical analysis using TLC and FT-IR spectroscopy
Figure 1. Anti-proliferative activity of ethanolic Citrus paradisi fruit extract.
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.