Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
14,866
datasets available to search
ShareScore release 0.9.0
Dataset results
14,866 results for “cancer cell”
Benchmarking Illumina RNA-seq fusion transcript detection methods - cancer cell lines RNA-seq
<p>Cancer cell line RNA-seq data (reads or names of reads from CCLE data) used for benchmarking Illumina-based fusion detection methods as used in:</p> <p>Haas, B.J., Dobin, A., Li, B. <em>et al.</em> Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. <em>Genome Biol</em> <strong>20</strong>, 213 (2019). https://doi.org/10.1186/s13059-019-1842-9</p> <p> </p> <p>For CCLE data, direct sharing of fastq files was not possible. CCLE data must be obtained from:</p> <p> https://portals.broadinstitute.org/ccle/home</p> <p>Instead, the identifiers for the reads leveraged as part of our study are made available, and these reads can be extracted from the CCLE fastq files directly once obtained from the primary source.</p> <p><br>For the non-CCLE data, the exact reads leveraged by our study are made directly available here in fastq format.</p>
Human pancreatic cancer single cell atlas reveals association of CXCL10+ fibroblasts and basal subtype tumor cells
Open the record for dataset details and reuse information.
Supplementary files for "Tristetraprolin Affects Invasion-Associated Genes Expression and Cell Motility in Triple-Negative Breast Cancer Model"
<p>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</p>
Flow cytometry data and image data -A dendritic cell vaccine for both vaccination and neoantigen-reactive T cell preparation for cancer immunotherapy in mice
Open the record for dataset details and reuse information.
The role of TAp63g and p53 point mutations in regulating DNA repair, mutational susceptibility and invasion of bladder cancer cell
<p>Raw data set for the manuscript submitted to e-Life (10-06-2021-RA-eLife-71184 ) for peer-review. </p>
Machine readable code lists for an algorithm to identify incident non-small cell lung cancer (NSCLC) in United States healthcare claims data
<p>Machine readable code lists for an algorithm to identify incident non-small cell lung cancer (NSCLC) in United States healthcare claims data</p>
HINC dataset from: Homeopathic treatment as an add-on therapy may improve quality of life and prolong survival in patients with non-small cell lung cancer: A prospective, randomized, placebo-controlled, double-blind, three-arm, multicenter study
<p class="CxSpFirst"><b>Background:</b> Patients with advanced non-small cell lung cancer (NSCLC) have limited treatment options. Alongside conventional anticancer treatment, additive homeopathy might help to alleviate side effects of conventional therapy. The aim of the present study was to investigate whether additive homeopathy might influence quality of life (QoL) and survival in NSCLC patients.</p> <p class="CxSpMiddle"><b>Methods:</b> In this prospective, randomized, placebo-controlled, double-blind, three-arm, multicenter, phase III study, we evaluated the possible effects of additive homeopathic treatment compared with placebo in NSCLC stage IV patients with respect to QoL in the two randomized groups and survival time in all three groups. Treated patients visited the outpatients' centers every 9 weeks. 150 Patients with stage IV NSCLC were included in the study. 98 received either individualized homeopathic remedies (n=51) or placebo (n=47) in a double-blinded fashion. 52 control patients without any homeopathic treatment were observed for survival only. The constituents of the different homeopathic remedies were mainly of plant, mineral or animal origin. The remedies were manufactured by stepwise dilution and succussion, thereby preparing stable Good Manufacturing Practice grade formulations.</p> <p class="CxSpMiddle"><b>Results:</b> QoL as well as functional and symptom scales showed significant improvement in the homeopathy group when compared with placebo after 9 and 18 weeks of homeopathic treatment (p<0.001). Median survival time was significantly longer in the homeopathy group (435 days) vs placebo (257 days; p=0.010) as well as vs control (228 days; p<0.001). Survival rate in the homeopathy group differed significantly from placebo (p=0.020) and from control (p<0.001).</p> <p class="CxSpMiddle"><b>Conclusion:</b> QoL improved significantly in the homeopathy group compared with placebo. In addition, survival was significantly longer in the homeopathy group versus placebo and control. A higher QoL might have contributed to the prolonged survival. The study suggests that homeopathy positively influences not only QoL but also survival. Further studies including other tumor entities are warranted.</p>
Cancer-Associated Fibroblast Classification in Single-Cell and Spatial Proteomics Data
<p>ometiff: Imaging Data</p> <p>Cell Masks: Masks generated with cellprofiler from ilastik segmentation training</p> <p>cp-output_config: All relevant cellprofiler output and additional configuration files (for example clinical data) necessary to generate the single cell experiments.</p> <p>IMC Data Objects: Single cell experiment RDS files.</p> <p> </p> <p>scRNA-seq_dataobjects: .Rds files containing the clustered breast cancer, colon cancer, HNSCC, NSCLC and PDAC datasets as well as the integrated validation dataset.</p>
The EGFR signaling modulates in mesenchymal stem cells the expression of miRNAs involved in the interaction with breast cancer cells
<p>We previously demonstrated that the epidermal growth factor receptor (EGFR) modulates in mesenchymal stem cells (MSCs) the expression of a number of genes coding for secreted proteins that promote breast cancer progression. However, the role of the EGFR in modulating in MSCs the expression of miRNAs potentially involved in the progression of breast cancer remains largely unexplored. Following small RNA-sequencing, we identified 36 miRNAs differentially expressed between MSCs untreated or treated with the EGFR ligand transforming growth factor α (TGFα), with a fold change (FC) <0.56 or FC ≥1.90 (CI, 95%). KEGG analysis revealed a significant enrichment in signaling pathways involved in cancer development and progression. EGFR activation in MSCs downregulated the expression of different miRNAs, including miR-23c. EGFR signaling also reduced the secretion of miR-23c in conditioned medium from MSCs. Functional assays demonstrated that miR-23c acts as tumor suppressor in basal/claudin-low MDA-MB-231 and MDA-MB-468 cells, through the repression of IL-6R. MiR-23c downregulation promoted cell proliferation, migration and invasion of these breast cancer cell lines. Collectively, our data suggested that the EGFR signaling regulates in MSCs the expression of miRNAs that might be involved in breast cancer progression, providing novel information on the mechanisms that regulate the MSC-tumor cell cross-talk.We previously demonstrated that the epidermal growth factor receptor (EGFR) modulates in mesenchymal stem cells (MSCs) the expression of a number of genes coding for secreted proteins that promote breast cancer progression. However, the role of the EGFR in modulating in MSCs the expression of miRNAs potentially involved in the progression of breast cancer remains largely unexplored. Following small RNA-sequencing, we identified 36 miRNAs differentially expressed between MSCs untreated or treated with the EGFR ligand transforming growth factor α (TGFα), with a fold change (FC) <0.56 or FC ≥1.90 (CI, 95%). KEGG analysis revealed a significant enrichment in signaling pathways involved in cancer development and progression. EGFR activation in MSCs downregulated the expression of different miRNAs, including miR-23c. EGFR signaling also reduced the secretion of miR-23c in conditioned medium from MSCs. Functional assays demonstrated that miR-23c acts as tumor suppressor in basal/claudin-low MDA-MB-231 and MDA-MB-468 cells, through the repression of IL-6R. MiR-23c downregulation promoted cell proliferation, migration and invasion of these breast cancer cell lines. Collectively, our data suggested that the EGFR signaling regulates in MSCs the expression of miRNAs that might be involved in breast cancer progression, providing novel information on the mechanisms that regulate the MSC-tumor cell cross-talk.</p>
Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers
<p>This repository contains the raw IMC data of ZTMA 26 as continuation of dataset <strong>10.5281/zenodo.7494413.</strong> The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of those parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files.</p> <p>Additionally, this repository contains the metadata of the patients analyzed in this study, the panel information and the single-cell data that was extracted from the multiplexed images together with the associated metadata in SingleCellExperiment format for analysis in R.</p> <p>The analysis.zip folder contains files that were written out during the analysis according to the scripts in https://github.com/BodenmillerGroup/BC_LN_metastses.</p> <p>The single-cell and other data outputs from CellProfiler can be found in the cpout.zip file.</p> <p>The IF_whole_sections.zip file contains the IF images of the primary breast cancer sections (czi files) and the extracted single-cell data.</p>
Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers
<p>This repository contains the raw IMC data of ZTMA 21 and 25 of the matched primary breast cancer and lymph node metastasis study presented in Fischer and Jackson et al., 2023. The code that was used to process and analyze this data can be found at https://github.com/BodenmillerGroup/BC_LN_metastses.</p> <p>The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of the respective parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files.</p>
The PLOD2/Succinate axis regulates the epithelial-mesenchymal plasticity and cancer cell stemness
<p>Aberrant accumulation of succinate has been detected in many cancers. However, the cellular function and regulation of succinate in cancer progression is not completely understood. Using stable isotope-resolved metabolomics (SIRM) analysis, we showed that the epithelial mesenchymal transition (EMT) was associated with profound changes in metabolites, including the elevation of cytoplasmic succinate levels. Treatment with cell-permeable succinate induced mesenchymal phenotypes in mammary epithelial cells and enhanced cancer cell stemness. Chromatin immunoprecipitation (ChIP) and sequence analysis showed that elevated cytoplasmic succinate levels were sufficient to reduce global 5-hydroxymethylcytosinene (5hmC) accumulation and induce transcriptional repression of EMT-related genes. We showed that expression of procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 (PLOD2) was associated with an elevation of cytoplasmic succinate during the EMT process. Silence of PLOD2 expression in breast cancer cells reduced succinate levels and inhibited cancer cell mesenchymal phenotypes and stemness, which was accompanied by elevated 5hmC levels in chromatin. Importantly, exogenous succinate rescued cancer cell stemness and 5hmC levels in PLOD2-silenced cells, suggesting that PLOD2 promotes cancer progression at least partially through succinate. These results reveal the previously unidentified function of succinate in enhancing cancer cell plasticity and stemness.</p> <p><em><strong><span></span></strong></em></p>
Annona squamosa Leaf Extract Inhibit Migration of Human Cervical Cancer Cells Through MMP-9 Expression
<p> Figure 1. a.<em>Annona squamosa</em> leaf . b.Simplicia powder of <em>Annona squamosa</em> leaves</p> <p>Figure 2. <em>Annona squamosa</em> leaves ethanol extract.</p> <p>Figure 3. FTIR spectrophotometer results of acetogenin compounds of<em> </em><em>Annona squamosa</em> leaves extract</p> <p>Figure 4. The cytotoxic test of HeLa cells at 24 hours. The combination of ASL (<em>Annona squamosa</em> leaf Extract) 12.5 mg/ml + cisplatin was very effective compared with a single therapy. *<em>P</em> < 0.05Figure 4. The cytotoxic test of HeLa cells at 24 hours. The combination of ASL (<em>Annona squamosa</em> leaf Extract) 12.5 mg/ml + cisplatin was very effective compared with a single therapy. *<em>P</em> < 0.05</p> <p>Figure 5. The percentage of living cells of HeLa cells were cultured with different concentrations of <em>Annona squamosa</em> leaf extract.</p> <p>Figure 6. The combination therapy of ASL with cisplatin reduced the expressions of MMP-9 in HeLa cells. a. A significant concentration for cytotoxicity was a concentration of 12.5 mg/mL ASL + 5 μg/mL Cisplatin. b. The number of MMP-9 positive cells. *<em>P< </em>0.005.</p> <p>Figure 7. The combination therapy of ASL and Cisplatin inhibit cell migration. a. HeLa cells were treated with single cisplatin or in combination with ASL 12.5; 25, 50, and a single dose of ASL 75 mg/mL. b. Percentage area of cells undergoing migration. *<em>P</em><0.005.</p> <p> </p> <p> </p>
processed single-cell data from "Cancer cell non-autonomous tumor progression from chromosomal instability"
<p>The h5ad files can be used as processed scRNA-seq input to the ContactTracing code (https://zenodo.org/badge/latestdoi/625036312).</p> <p>There is one file for the highCIN/lowCIN comparison, and another for the highCIN/noSTING comparison.</p>
Characterising neutrophil subtypes in cancer using human and murine single-cell RNA sequencing datasets
<p>Single cell RNA sequencing data generated by 10xGenomics for Neutrophils derived from colorectal cancer (CRC) KPN tumours (CRC_KPN_counts.csv) and normalised counts (CRC_KPN_NormalisedCounts.csv) as well as from other mouse models of CRC carrying AKPT, BPN, BP and KP mutations (CRC_other_counts.csv and CRC_other_NormalisedCounts.csv), together with the relevant metadata (CRC_KPN_metadata.csv and CRC_other_metadata.csv).</p>
Single Cell RNA sequencing data of ADT treated Prostate cancer patients
<p>The data was generated from a study that was conducted according to guidelines approved by the Review Board at the University of Texas Southwestern Medical Center. We procured patient biopsy samples from two distinct studies. The first is titled "Tissue Collection and Results Gathering for Radiotherapy Patients & Healthy Individuals" (STU 072010-098), and the second is a Phase I Clinical Study on Stereotactic Ablative Radiotherapy (SABR) for Pelvic and Prostate Areas in High-Risk Prostate Cancer Patients (STU062014-027). The single-cell RNA sequencing (scRNA-seq) took place in Dr. Douglas Strand's laboratory, adhering to the method outlined in Henry et al<sup>1</sup>. We used a 1-hour treatment with 5mg/ml of collagenase type I, 10mM of ROCK inhibitor, and 1mg of DNase. Barcode labeling for 3' GEX was done using a 10X machine, and the sequencing process utilized an Illumina NextSeq 500 device.</p> <p> </p> <p>1. Henry, G. H., Malewska, A., Joseph, D. B., Malladi, V. S., Lee, J., Torrealba, J., ... & Strand, D. W. (2018). A cellular anatomy of the normal adult human prostate and prostatic urethra. <em>Cell reports</em>, <em>25</em>(12), 3530-3542.</p>
Rovalpituzumab Tesirine (SC16LD6.5) in Recurrent Small Cell Lung Cancer
ClinicalTrials.gov study NCT01901653. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Sorafenib in Treating Patients With Extensive Stage Small Cell Lung Cancer
ClinicalTrials.gov study NCT00182689. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cisplatin/Carboplatin and Etoposide With or Without Nivolumab in Treating Patients With Extensive Stage Small Cell Lung Cancer
ClinicalTrials.gov study NCT03382561. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Study of Atezolizumab Plus Carboplatin and Etoposide With or Without Tiragolumab in Patients With Untreated Extensive-Stage Small Cell Lung Cancer
ClinicalTrials.gov study NCT04256421. IPD Sharing: YES. Countries: 23. Publications: 1.
ScienceDex guides
Understand access before you commit
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.