5500 results for "*oma"

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• Mapping the lineage-retained antigen landscape in neuroblastoma

  Neuroblastoma is among the deadliest pediatric solid tumors, and relapse is frequently driven by lineage plasticity between adrenergic (ADRN) and mesenchymal (MES) cell states that escape conventional and targeted therapies. This project aims to identify tumor antigens that are retained across both lineage states and are therefore suitable for T-cell–based immunotherapy resistant to lineage switching, including non-canonical antigens derived from the "dark proteome." To support this aim, we generated paired RNA-sequencing and ribosome profiling (Ribo-seq) data from neuroblastoma cell lines, patient-derived tumor organoids, and primary patient tumors spanning ADRN and MES states. The RNA-seq data enable custom transcriptome assembly to recover non-reference and non-canonical transcripts, while Ribo-seq maps actively translated canonical and non-canonical open reading frames at codon resolution. Together these data provide the molecular substrate for systematic discovery of lineage-retained, translation-supported neuroblastoma antigens.

  Study EGAS00001008445

• Orthotopic Patient-Derived Organoid Model Reveals Tumor Microenvironment-Dependent Phenotypes in Lung Squamous Cell Carcinoma

  This dataset contain NGS raw fastq data from 27 samples, including 5 WES, 4 WGS, 1 shallow WGS(sWGS) and 17 RNAseq.

  Dataset EGAD50000002915

• Multi-modal single-cell sequencing dataset for large B cell lymphoma samples

  This dataset contains raw FASTQ sequencing data from single-cell transcriptome, BCR, TCR, and HTO profiling of 72 hashtag-multiplexed large B-cell lymphoma samples, generated using the 10x Genomics Chromium Single Cell 5′ workflow and sequenced on an Illumina NextSeq 2000.

  Dataset EGAD50000002966

• scRNA-seq data from HNSCC samples before and after BA treatment

  Tumor biopsies from 6 head and neck small cell carcinoma (HNSCC) berfore and 3-weeks after bintrafusp-alfa treatment were analyzed using single-cell RNA sequencing (droplet-based 3' 10x genomics). Library were sequenced using the Chromium plateform. Generated fastq files were processed using cellranger to generat the count matrices.

  Dataset EGAD50000003043

• Low-coverage whole-genome sequencing

  Low-coverage whole-genome sequencing from CSF samples collected across timepoints from medulloblastoma patients

  Dataset EGAD50000003058

• Gut microbiota biomarkers associated with Multiple Myeloma: The REMNANT Study

  This dataset contains longitudinal shotgun metagenomic sequencing of stool samples collected across two time points from patients with newly diagnosed multiple myeloma (153 patients , 306 samples total). The suffix "scr" denotes the screening time point, when patients were enrolled in the study and samples were collected before initiation of treatment. Following inclusion, patients received standard multiple myeloma treatment according to Norwegian clinical guidelines. The treatment consisted of four cycles of induction therapy with bortezomib, lenalidomide, and dexamethasone (VRd), followed by autologous stem cell transplantation (ASCT) for eligible patients, and subsequently four cycles of consolidation therapy with VRd. The second stool sample was collected after completion of consolidation therapy. Therefore, samples with the suffix "post_con" represent the post-consolidation time point. This is the time point which MRD was measured. Samples were sequenced on the Illumina NovaSeq X platform. Raw data consists of paired FASTQ files per sample.

  Dataset EGAD50000003072

• Norwegian Sarcoma Consortium Tumor-Normal pairs Whole Exome Sequencing dataset 2026

  The dataset consist of Whole Exome Sequencing results from 287 sarcoma patients in the NoSarC cohort, from which matched sarcoma tumor samples and normal blood samples where pairwise analysed together using the Dragen v.3.7 analysis framework. The dataset contains fastq files as used for input to the analysis and the Dragen 3.7 vcfs outputs for germline mutations, somatic mutations and copy number variants (and their corresponding index files). The phenotype information provided includes: age, sex, times of birth, surgery, death, last followup or last known alive, local recurrence assessment, metastatic-free survival assessment and reccurence-free survival assessment. All times provided in a month-year format. 8 disease and topography fields such as disease status at inclusion, time of WES tumor sampling and final histological diagnosis, as well as tumor lesion sampled and localization of the sarcoma in final diagnosis, are inluced, as well as 5 outcome-related variables incl overall survival and cause of death. Finally 5 treatment-related variables are included. Due to high sequencing depth in several samples, the provided fastq files is the result of a screening process and downsampling if nessearcy, done before the Dragen analysis. The procedure is documented in the included README_fastq_downsampling.txt

  Dataset EGAD50000003102

• Carcinoma of Unknown Primary (CUP): A comparison across tissue and liquid biomarkers (CUP-COMP) study

  The Carcinoma of Unknown Primary (CUP): A comparison across tissue and liquid biomarkers (CUP-COMP) study (NCT: NCT04750109) was sponsored by The Christie NHS Foundation Trust and funded by Innovate UK.

  Study EGAS50000001821

• A single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  Nodal B-cell non-Hodgkin lymphomas (B-NHL) are a clinically diverse set of cancers thought to originate from distinct stages of B-cell maturation. To characterize intratumor heterogeneity across B-NHL entities, we performed CITE-Seq (cellular indexing of transcriptomes and epitopes) on 51 lymph node samples including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL, n = 11) tumors, in addition to non-malignant reactive lymph nodes (rLN, n = 8). We also performed 5 prime scRNA-seq with immune receptor profiling for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL, and 2 MZL).

  Study EGAS50000000342

• Leeds Melanoma Cohort (LMC) gene expression study

  Array-based profiling (whole genome DASL HT12.4, Illumina Inc) in over 700 FFPE tumour blocks from the population-based Leeds Melanoma cohort recruited in the North of England, with a long follow up. Data used in tumour immune micro-environment investigation (Nsengimana et al 2018, J Clin Invest doi: 10.1172/JCI95351).

  Study EGAS00001002922