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1,258 results for “neuroblastoma”
Dataset of "TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth"
<p>The embryonic transcription factors TWIST1/2 are frequently overexpressed in cancer, acting as multifunctional oncogenes. Here we investigate their role in neuroblastoma (NB), a heterogeneous childhood malignancy ranging from spontaneous regression to dismal outcomes despite multimodal therapy. We first reveal the association of TWIST1 expression with poor survival and metastasis in primary NB, while TWIST2 correlates with good prognosis. Secondly, suppression of TWIST1 by CRISPR/Cas9 results in a reduction of tumor growth and metastasis in immunocompromised mice. Moreover, TWIST1 knock-out tumors displays a less aggressive cellular morphology and a reduced disruption of the extracellular matrix (ECM) reticulin network. Additionally, we identify a TWIST1-mediated transcriptional program associated with dismal outcome in NB and involved in the control of pathways mainly linked to the signaling, migration, adhesion, the organization of the ECM, and the tumor cells versus tumor stroma crosstalk. Taken together, our findings identified TWIST1 as novel therapeutic target in NB.</p>
Dataset for "TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth"
<p>The embryonic transcription factors TWIST1/2 are frequently overexpressed in cancer, acting as multifunctional oncogenes. Here we investigate their role in neuroblastoma (NB), a heterogeneous childhood malignancy ranging from spontaneous regression to dismal outcomes despite multimodal therapy. We first reveal the association of TWIST1 expression with poor survival and metastasis in primary NB, while TWIST2 correlates with good prognosis. Secondly, suppression of TWIST1 by CRISPR/Cas9 results in a reduction of tumor growth and metastasis in immunocompromised mice. Moreover, TWIST1 knock-out tumors displays a less aggressive cellular morphology and a reduced disruption of the extracellular matrix (ECM) reticulin network. Additionally, we identify a TWIST1-mediated transcriptional program associated with dismal outcome in NB and involved in the control of pathways mainly linked to the signaling, migration, adhesion, the organization of the ECM, and the tumor cells versus tumor stroma crosstalk. Taken together, our findings confirm TWIST1 as promising therapeutic target in NB.</p> <p>This dataset comprise images (.ndpi files) of anti-F4/80 IHC staining used for the quantification of macrophages in subcutaneous and orthotopic neuroblastoma xenografts derived from SK-N-Be2c cells expressing TWIST1 or knocked out for TWIST1 through CRISR/Cas9.</p>
Additional data: Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring
<p>This repository provides additional data for the manuscript titled "Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring", currently under revision at Nature Genetics. The primary data cohort has been deposited in the HTAN data portal. This repository includes processed 10x Xenium spatial transcriptomic data for six TH-MYCN mice (three chemotherapy-treated and three treatment-naive) as well as processed scRNA-seq data for CHLA15 and CHLA20 neuroblastoma (NBL) cells. The scRNA-seq data includes mono-cultured, co-cultured cells with THP-1 macrophages, and co-culture cells treated with Afatinib/CRM197. </p>
Graph topological features extracted from expression profiles of neuroblastoma patients
<p><strong>Introduction</strong></p> <p>This dataset contains the data described in the paper titled "A deep neural network approach to predicting clinical outcomes of neuroblastoma patients." by Tranchevent, Azuaje and Rajapakse. More precisely, this dataset contains the topological features extracted from graphs built from publicly available expression data (see details below). This dataset does not contain the original expression data, which are available elsewhere. We thank the scientists who did generate and share these data (please see below the relevant links and publications).</p> <p> </p> <p><strong>Content</strong></p> <p>File names start with the name of the publicly available dataset they are built on (among "Fischer", "Maris" and "Versteeg"). This name is followed by a tag representing whether they contain raw data ("raw", which means, in this case, the raw topological features) or TF formatted data ("TF", which stands for TensorFlow). This tag is then followed by a unique identifier representing a unique configuration. The configuration file "Global_configuration.tsv" contains details about these configurations such as which topological features are present and which clinical outcome is considered.</p> <p>The code associated to the same manuscript that uses these data is at <a href="https://gitlab.com/biomodlih/SingalunDeep">https://gitlab.com/biomodlih/SingalunDeep</a>. The procedure by which the raw data are transformed into the TensorFlow ready data is described in the paper.</p> <p> </p> <p><strong>File format</strong></p> <p>All files are TSV files that correspond to matrices with samples as rows and features as columns (or clinical data as columns for clinical data files). The data files contain various sets of topological features that were extracted from the sample graphs (or Patient Similarity Networks - PSN). The clinical files contain relevant clinical outcomes.</p> <p>The raw data files only contain the topological data. For instance, the file "Fischer_raw_2d0000_data_tsv" contains 24 values for each sample corresponding to the 12 centralities computed for both the microarray (<em>Fischer-M</em>) and RNA-seq (<em>Fischer-R</em>) datasets. The TensorFlow ready files do not contain the sample identifiers in the first column. However, they contain two extra columns at the end. The first extra column is the sample weights (for the classifiers and because we very often have a dominant class). The second extra column is the class labels (binary), based on the clinical outcome of interest.</p> <p> </p> <p><strong>Dataset details</strong></p> <p>The <em>Fischer</em> dataset is used to train, evaluate and validate the models, so the dataset is split into train / eval / valid files, which contains respectively 249, 125 and 124 rows (samples) of the original 498 samples. In contrast, the other two datasets (<em>Maris</em> and <em>Versteeg</em>) are smaller and are only used for validation (and therefore have no training or evaluation file).</p> <p>The <em>Fischer</em> dataset also has more data files because various configurations were tested (see manuscript). In contrast, the validation, using the <em>Maris</em> and <em>Versteeg</em> datasets is only done for a single configuration and there are therefore less files.</p> <p>For <em>Fischer</em>, a few configurations are listed in the global configuration file but there is no corresponding raw data. This is because these items are derived from concatenations of the original raw data (see global configuration file and manuscript for details).</p> <p> </p> <p><strong>References</strong></p> <p>This dataset is associated with Tranchevent L., Azuaje F.. Rajapakse J.C., A deep neural network approach to predicting clinical outcomes of neuroblastoma patients.</p> <p>If you use these data in your research, please do not forget to also cite the researchers who have generated the original expression datasets.</p> <p><em>Fischer</em> dataset:</p> <ul> <li>Zhang W. et al., Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biology 16(1) (2015). doi:10.1186/s13059-015-0694-1</li> <li>Wang C. et al., The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat. Biotechnol. 32(9), 926–932. doi:10.1038/nbt.3001</li> </ul> <p><em>Versteeg</em> dataset:</p> <ul> <li>Molenaar J.J. et al., Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature 483(7391), 589–593. doi:10.1038/nature10910</li> </ul> <p><em>Maris</em> dataset:</p> <ul> <li>Wang Q. et al., Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number. Cancer Res. 66(12), 6050–6062. doi:10.1158/0008-5472.CAN-05-4618</li> </ul>
Conceptual Model of Neuroblastoma
<p>The following is the Neuroblastoma Conceptual Model (CMN) resulting from the study of the domain and collaborative meetings with clinical experts at Hospital <em>Hospital Universitari y Politècnic de La Fe</em>. Based on a previous CMN [1], the analysis of each of the classes has been carried out, structured in views and extended to adapt it to the new knowledge of the domain.</p>
Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging
<p>MELC (Multi-epitope ligand cartography) multiplex imaging data of our neuroblastoma cohort supporting the publication " Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging". The zip folders contain raw image data of one to four fields of view (FoV). The folder "RoI" contains the masks of user-selected regions. "marker_status.csv" is used for normalization with RESTORE. "MELC_single_cell_data.csv" contains the normalized single-cell data with cell type assignments.</p>
Supporting data for "Dissecting the cellular architecture of neuroblastoma bone marrow metastasis using single-cell transcriptomics and epigenomics unravels the role of monocytes at the metastatic niche"
<p>This data repository contains several datasets supplementing the paper “Dissecting the cellular architecture of neuroblastoma bone marrow metastasis using single-cell transcriptomics and epigenomics unravels the role of monocytes at the metastatic niche” by Fetahu, Esser-Skala, Dnyansagar et al. (2023).</p> <ul> <li>HOMER_Results.zip: detailed results of the HOMER analysis</li> <li>nblast_scopen_gene_activity_normalized_motifs_added.rds: Seurat object with scATAC-seq data</li> <li>snp_array.tgz: SNP array data</li> <li>R_data_generated.tgz: Files generated by the scRNA-seq analysis scripts in the GitHub repository associated with the publication.</li> </ul>
Neuroblastoma cell lines display heterogeneity in differentiation responses
<p>Underlying and extended data for the manuscript "Neuroblastoma cell lines display heterogeneity in differentiation responses", Ferguson et al (2024). Includes Underlying data for Figures 2A-C and Figures 3A-D, and Extended data - Table S1: qRT-PCR primer sequences, Table S2 - List of genes in clusters identified in [7] (Table S2 added after version 1).</p>
Chromosomal instability degrades developmental phenotypes essential for anti-GD2 immunotherapy outcomes in high-risk neuroblastoma
<p>Childhood Cancer Data Initiative (CCDI)<br>dbGaP Study Accession: phs002431</p>
3F8/GM-CSF Immunotherapy Plus 13-Cis-Retinoic Acid for Primary Refractory Neuroblastoma in Bone Marrow
ClinicalTrials.gov study NCT01183897. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cyclophosphamide and Prednisone With or Without Immunoglobulin in Treating Abnormal Muscle Movement in Children With Neuroblastoma
ClinicalTrials.gov study NCT00033293. IPD Sharing: Not stated. Countries: 3. Publications: 1.
Irinotecan and Temozolomide in Treating Young Patients With Recurrent Neuroblastoma
ClinicalTrials.gov study NCT00311584. IPD Sharing: Not stated. Countries: 3. Publications: 1.
Therapy for Children With Advanced Stage Neuroblastoma
ClinicalTrials.gov study NCT01857934. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Irinotecan Hydrochloride and Temozolomide With Temsirolimus or Dinutuximab in Treating Younger Patients With Refractory or Relapsed Neuroblastoma
ClinicalTrials.gov study NCT01767194. IPD Sharing: Not stated. Countries: 5. Publications: 3.
3F8/GM-CSF Immunotherapy Plus 13-Cis-Retinoic Acid for Consolidation of First Remission After Non-Myeloablative Therapy in Patients With High-Risk Neuroblastoma
ClinicalTrials.gov study NCT01183429. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Sodium Thiosulfate in Preventing Hearing Loss in Young Patients Receiving Cisplatin for Newly Diagnosed Germ Cell Tumor, Hepatoblastoma, Medulloblastoma, Neuroblastoma, Osteosarcoma, or Other Malignan
ClinicalTrials.gov study NCT00716976. IPD Sharing: Not stated. Countries: 3. Publications: 1.
Monoclonal Antibody 3F8 and Sargramostim in Treating Patients With Neuroblastoma
ClinicalTrials.gov study NCT00072358. IPD Sharing: Not stated. Countries: 1. Publications: 2.
hu14.18-Interleukin-2 Fusion Protein in Treating Young Patients With Recurrent or Refractory Neuroblastoma
ClinicalTrials.gov study NCT00082758. IPD Sharing: Not stated. Countries: 2. Publications: 2.
Phase 2 Study of Bintrafusp Alfa in Recurrent/Metastatic Olfactory Neuroblastoma (BARON).
ClinicalTrials.gov study NCT05012098. IPD Sharing: YES. Countries: 1. Publications: 1.
Combination Chemotherapy and Surgery With or Without Isotretinoin in Treating Young Patients With Neuroblastoma
ClinicalTrials.gov study NCT00499616. IPD Sharing: Not stated. Countries: 6. Publications: 2.
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.
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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.