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1,615 results for “tumour”
Pan-cancer analysis of mRNA stability for decoding tumour post-transcriptional programs
<p>Supplemental data and analysis files for Perron et al.: "Pan-cancer analysis of mRNA stability for decoding tumour post-transcriptional programs" (<a href="https://www.nature.com/articles/s42003-022-03796-w">https://www.nature.com/articles/s42003-022-03796-w</a>). The .tar.gz files contain read counts associated with various RNA-seq analyses. The .rds files are single R object files that contain various analysis results tables. The .csv files also contain analysis results or sample metadata tables. See <a href="http://csg.lab.mcgill.ca/sup/pancancer_stability/">http://csg.lab.mcgill.ca/sup/pancancer_stability/</a> for a full description of the files.</p>
Logical model for Molecular Pathways Enabling Tumour Cell Invasion and Migration
<p>Understanding the etiology of metastasis is very important in clinical perspective, since it is estimated that metastasis accounts for 90% of cancer patient mortality. Metastasis results from a sequence of multiple steps including invasion and migration. The early stages of metastasis are tightly controlled in normal cells and can be drastically affected by malignant mutations; therefore, they might constitute the principal determinants of the overall metastatic rate even if the later stages take long to occur. To elucidate the role of individual mutations or their combinations affecting the metastatic development, a logical model has been constructed that recapitulates published experimental results of known gene perturbations on local invasion and migration processes, and predict the effect of not yet experimentally assessed mutations. The model has been validated using experimental data on transcriptome dynamics following TGF-β-dependent induction of Epithelial to Mesenchymal Transition in lung cancer cell lines. A method to associate gene expression profiles with different stable state solutions of the logical model has been developed for that purpose. In addition, we have systematically predicted alleviating (masking) and synergistic pairwise genetic interactions between the genes composing the model with respect to the probability of acquiring the metastatic phenotype. We focused on several unexpected synergistic genetic interactions leading to theoretically very high metastasis probability. Among them, the synergistic combination of Notch overexpression and p53 deletion shows one of the strongest effects, which is in agreement with a recent published experiment in a mouse model of gut cancer. The mathematical model can recapitulate experimental mutations in both cell line and mouse models. Furthermore, the model predicts new gene perturbations that affect the early steps of metastasis underlying potential intervention points for innovative therapeutic strategies in oncology.</p> <p> </p> <p>Included files:</p> <ul> <li>Master Model: the model includes detailed regulation of the major players involved in the crosstalks between Notch and p53 pathways</li> <li>Modular Model: the model is a reduction of the master model. To reduce the master model, we lumped together some entities that belonged to a module.</li> </ul>
bulk-tumour-api: a programmatically accessible dataset of pre-processed bulk tumour sequencing data
<p><strong>This repository, including the API, are currently under development.</strong></p> <p><strong>bulk-tumour-api</strong>: A programmatically accessible dataset of pre-processed bulk tumour sequencing data. The python API can be found at https://github.com/tomouellette/bulk-tumour-api. All data stored in this repository have been collected from open access online sources. Original references and sources are provided in database.tsv (for empirical patient data) and synthetic.tsv (for simulated data).</p> <p><strong>A note on datasets: </strong></p> <ul> <li>All <em>empirical patient sequencing </em>samples have been processed into pseudo-VCF files which at minimum contain the following columns: sample identifier (sample), patient identifier (patient), chromosome (chr), position (pos), variant allele frequency (VAF), alternate read counts (t_alt_count), depth (DP), and total copy number (total_cn). However, if more data is required, unprocessed data including copy number segments or gene-level calls, clinical, and/or biopsy level information can be found in the /raw/. </li> <li>All <em>synthetic datasets </em>have also been processed in pseudo-VCF files. In some cases, all ground truth information (e.g. subclone frequency) is contained within the pseudo-VCF. In other cases, additional meta/ground-truth information are in separate files; any simulated sample with a column marked has_meta = True will have multiple files that will be downloaded together.</li> </ul>
Data: multimodal cell tracking from systemic administration to tumour growth by combining gold nanorods and reporter genes
<p>This data set includes multispectral optoacoustic tomography images supporting an article on cell tracking (preprint: bioRxiv 199836; https://doi.org/10.1101/199836). The corresponding bioluminescence results are included too, as well as the spectra used for the multispectral processing. </p>
Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer - pre-processed data
<p>A multicentre, prospective observational study was conducted of colorectal cancer (CRC) patients undergoing primary surgical resection in the United Kingdom and Czech Republic. Analysis was performed using metataxonomics (microbiome) and ultra-performance liquid chromatography mass spectrometry (UPLC-MS, metabolomics). Both datasets were pre-processed as described in the methods section of the main article. The data here were used as the input to the data analysis workflows available from <a href="https://github.com/jmp111/CRC">Github</a>.</p>
ASPH and Hypoxia Marker Expression in Head and Neck Carcinomas: Implications for HPV-Associated Tumours
<p><strong>Data open:</strong> file with parametres used for the multivariate evaluation. </p>
Molecular Signatures of Tumour and its Microenvironment for Precise Quantitative Diagnosis of Oral Squamous Cell Carcinoma: An Interna-tional Multi-cohort Diagnostic Validation Study
<p><strong>Supplementary Materials: </strong>The following supporting information can be downloaded at: www.mdpi.com/xxx/s1, <strong>Table ST1</strong> – qMIDS<sup>V2 </sup>Gene panel primer sequences; <strong>Figure S1</strong> – qMIDS<sup>V1</sup> vs qMIDS<sup>V2</sup> 384-well assay format and protocols; <strong>Figure S2.</strong> Individual target gene expression pattern in 1761 samples; <strong>Figure S3.</strong> Various statistical methods used for gene selection analysis on 1761 clinical samples; <strong>Figure S4. </strong>Diagnostic performance comparison between qMIDS<sup>V2</sup> vs qMIDS<sup>V2* </sup>(with 4 less effective genes removed from the panel of 14 target genes of qMIDS<sup>V2</sup>); <strong>Figure S5</strong>. Effect of removing individual genes from the 14-target gene panel qMIDS<sup>V2</sup> (qV2) on diagnostic test performance based on the UK patient cohort data.</p>
Processed data for "Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses"
<p>tar.gz of processed data in the form of compressed R files (rds) of SingleCellExperiment (<a href="https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html">https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html</a>) objects and a metadata csv for the data in the publication <em>Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses </em>(O'Flanagan et al. 2019).</p>
Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma
<p>These are whole-slide digital pathology images of esophageal adenocarcinoma (EAC) patient-derived xenograft models. EAC biopsy specimens were cultured <em>in vitro</em> before implanting into immuno-deficient mice. Mice were then divided into the following treatment groups and treated with combinations of chemotherapy and PDE5 inhibitors as follows:</p> <ol> <li>Untreated</li> <li>Epirubicin + Cisplatin + Capecitabine (ECX)</li> <li>ECX + Vardenafil</li> <li>ECX + Tadalafil</li> </ol> <p>All whole slide images are in Olympus .vsi format and can be opened using the BioFormats library in QuPath. We have also included classifiers and scripts for performing the digital pathology analysis in QuPath, and information to link each mouse with treatment groups and corresponding whole slide images.</p> <p>File metadata:</p> <p>classifiers.zip - Folder containing pixel classifiers used for segmentation of IHC stains. These classifiers are to be important into QuPath for the respective analysis of Periostin (POSTN) and alpha Smooth Muscle Actin (SMA) staining using the included Groovy scripts in the scripts folder.</p> <p>SMA.zip - Folder containing whole slide images of mouse patient-derived xenograft tumours in .vsi format (Olympus VS110). Immunohistochemistry with anti-alpha Smooth Muscle Actin antibody.<br> POSTN.zip - Folder containing whole slide images of mouse patient-derived xenograft tumours in .vsi format (Olympus VS110). Immunohistochemistry with anti-Periostin antibody.</p> <p>scripts.zip - Folder containing all groovy scripts used in QuPath for tissue detection (Whole Section Tissue Detection.groovy), and segmentation of POSTN (POSTN Quantification Mice.groovy) and SMA staining tissue areas (SMA Quantification Mice.groovy).</p> <p>POSTN.xlsx - Data on the mice for which anti-POSTN IHC is available. Column names as follows:<br> Image: file name (corresponding to .vsi file).<br> Mouse_ID: Mouse identifier.<br> Treatment: Treatment administered. ECX - Epirubicin, Cisplatin and Capecitabine.<br> POSTN_Area: Total measured area of POSTN+ tissue in the tissue section (in um^2).<br> Total_Area: Total area of the tissue section (in um^2).<br> percentage_POSTN: Percentage of total tissue area that is stained with POSTN (%).</p> <p>SMA.xlsx - Data on the mice for which anti-SMA IHC is available. Column names as follows:<br> Image: file name (corresponding to .vsi file).<br> Mouse_ID: Mouse identifier.<br> Treatment: Treatment administered. ECX - Epirubicin, Cisplatin and Capecitabine.<br> SMA_Area: Total measured area of SMA+ tissue in the tissue section (in um^2).<br> Total_Area: Total area of the tissue section (in um^2).<br> percentage_SMA: Percentage of total tissue area that is stained with SMA (%).</p>
Ultrasound Stochastic Tomography simulation data for In-silico 2D Breast Phantom model with tumour
<p>An anatomically realistic numerical breast phantom model (with realistic acoustic properties of speed of sound, density, and attenuation coefficient of tissues) derived from [1] is presented with details of a ultrasound tomography experiment in simulation. Details of source wavelets, geometry of transducer set, observed data at each transducer for each shots are provided with phantom model.</p> <p>References</p> <p>[1] <a href="https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/">https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/</a></p>
Fig. 2 in Anti-tumour necrosis factor activity in saliva of various tick species and its appearance during the feeding period
Fig. 2. Anti-tumour necrosis factor (TNF) activity in tick salivary glands during feeding. Salivary gland extract (SGE) was prepared from females of Ixodes ricinus (Linnaeus, 1758) either unfed (day 0) or fed for 2, 4, 6 and 8 days. Various concentrations of SGE protein were preincubated for 1.5 h with 2 ng/ml of mouse recombinant TNF before the cytokine ELISA was performed. PBS instead of SGE was added into negative control. Results are presented as the mean ± SD of triplicate wells. *The difference between saliva-treated and untreated group was signif- icant at P <0.05.
A Study Comparing Treatment With 177Lu-DOTA0-Tyr3-Octreotate to Octreotide LAR in Patients With Inoperable, Progressive, Somatostatin Receptor Positive Midgut Carcinoid Tumours
ClinicalTrials.gov study NCT01578239. IPD Sharing: YES. Countries: 8. Publications: 4.
Study of Lanreotide Autogel 120 mg in Patients With Non-functioning Entero- Pancreatic Endocrine Tumour
ClinicalTrials.gov study NCT00842348. IPD Sharing: YES. Countries: 9. Publications: 2.
Study of Lanreotide Autogel in Non-functioning Entero-pancreatic Endocrine Tumours
ClinicalTrials.gov study NCT00353496. IPD Sharing: YES. Countries: 15. Publications: 3.
A Study to Observe Vedolizumab and Anti-tumour Necrosis Factors (Anti-TNFs) Outcomes in Real-world Biologic Ulcerative Colitis (UC) and Crohn's Disease (CD) Participants
ClinicalTrials.gov study NCT03710486. IPD Sharing: YES. Countries: 2. Publications: 1.
Reproducibility archive for MeDIP analyses of plasma DNA from brain tumour patients.
<p>This contains the starting points, intermediate objects, and the code used to produce them that were used to generate the figures in the associated paper. For execution, please extract the contents of both the data and the markdowns/scripts folder into the same folder. </p>
Link to dataset related to article "Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth "
<p>This record contains raw data related to article “ Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth"</p> <p>The microbiota has been shown to promote intestinal tumourigenesis, but a possible anti-tumourigenic effect has also been postulated. Here, we demonstrate that changes in the microbiota and mucus composition are concomitant with tumourigenesis. We identified two anti-tumourigenic strains of the microbiota-Faecalibaculum rodentium and its human homologue, Holdemanella biformis-that are strongly under-represented during tumourigenesis. Reconstitution of Apc<sup>Min/+</sup> or azoxymethane- and dextran sulfate sodium-treated mice with an isolate of F. rodentium (F. PB1) or its metabolic products reduced tumour growth. Both F. PB1 and H. biformis produced short-chain fatty acids that contributed to control protein acetylation and tumour cell proliferation by inhibiting calcineurin and NFATc3 activation in mouse and human settings. We have thus identified endogenous anti-tumourigenic bacterial strains with strong diagnostic, therapeutic and translational potential.</p>
Dataset related to article "Evaluation of cell metabolic adaptation in wound and tumour by fluorescence Lifetime imaging Microscopy"
<p>This record contains data related to article "Evaluation of cell metabolic adaptation in wound and tumour by fluorescence Lifetime imaging Microscopy"</p> <p>Abstract</p> <p>Acidic pH occurs in acute wounds progressing to healing as consequence of a cell metabolic adaptation in response to injury-induced tissue hypoperfusion. In tumours, high metabolic rate leads to acidosis affecting cancer progression. Acidic pH affects activities of remodelling cells in vitro. The pH measurement predicts healing in pathological wounds and success of surgical treatment of burns and chronic ulcers. However, current methods are limited to skin surface or based on detection of fluorescence intensity of specific sensitive probes that suffer of microenvironment factors. Herein, we ascertained relevance in vivo of cell metabolic adaptation in skin repair by interfering with anaerobic glycolysis. Moreover, a custom-designed skin imaging chamber, 2-Photon microscopy (2PM), fluorescence lifetime imaging (FLIM) and data mapping analyses were used to correlate maps of glycolytic activity in vivo as measurement of NADH intrinsic lifetime with areas of hypoxia and acidification in models of skin injury and cancer. The method was challenged by measuring the NADH profile by interfering with anaerobic glycolysis and oxidative phosphorylation in the mitochondrial respiratory chain. Therefore, intravital NADH FLIM represents a tool for investigating cell metabolic adaptation occurring in wounds, as well as the relationship between cell metabolism and cancer.</p>
A model for the dissemination of circulating tumour cell clusters involving platelet recruitment and a plastic switch between cooperative and individual behaviours
<p>This folder includes live/dead cell counts as well as transwell assay data for the corresponding manuscript. </p>
Genomic signature for malignant tumour progression in cervical cancer
<p>To investigate the clinical genomic signatures associated with tumor progression, we performed genomic sequencing on patients with cervical cancer, including primary, recurrent, and metastatic tumor tissues, and obtained their somatic mutation and copy number alteration profiles.</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.