5495 results for "*oma"

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• RNA-Seq dataset of Targeting the dark proteome to expand the lineage-retained antigen landscape in neuroblastoma

  This dataset contains bulk RNA-sequencing data generated to enable custom transcriptome assembly and to provide expression context for matched ribosome profiling in the discovery of lineage-retained neuroblastoma tumor antigens. RNA was sequenced from 183 neuroblastoma samples comprising cell lines, patient-derived tumor organoids, and primary patient tumors spanning the adrenergic (ADRN) and mesenchymal (MES) lineage states, with 101 samples prepared as rRNA-depleted (total RNA) libraries and 82 samples prepared as poly(A)-selected libraries. Libraries were sequenced paired-end (2x150 bp) on the Illumina NovaSeq 6000 platform. Raw data are provided as paired-end fastq.gz files.

  Dataset EGAD00001016124

• Ribo-Seq dataset of Targeting the dark proteome to expand the lineage-retained antigen landscape in neuroblastoma

  This dataset contains ribosome profiling (Ribo-seq) data generated to map actively translated open reading frames, including non-canonical ORFs from the "dark proteome", in neuroblastoma, supporting the identification of translation-validated tumor antigens. Ribosome-protected mRNA fragments (~28–30 nt) were isolated from 47 neuroblastoma samples comprising cell lines, patient-derived tumoroids, and primary patient tumors spanning the adrenergic (ADRN) and mesenchymal (MES) lineage states. Libraries were prepared following a modified version of the McGlincy & Ingolia 2017 protocol and sequenced single-end (1x50 bp) on the Illumina NextSeq 2000 platform. Raw data are provided as single-end fastq.gz

  Dataset EGAD00001016123

• GBM-Space: Transcriptomic Profiling of Patient-Derived Glioblastoma Cell Lines (Parse Biosciences - Evercode WT)

  Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This dataset comprises sequencing data from single-cell transcriptomic profiles of patient-derived glioblastoma cell lines (Parse Biosciences Evercode WT v3), towards experimentally validating the malignant cell trajectory from developmental-like to gliosis-hypoxia states.

  Dataset EGAD00001016126

• Genome and transcriptome sequence data from a laryngeal squamous cell carcinoma patient

  Genome and transcriptome sequence data from a laryngeal squamous cell carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016127

• Genome and transcriptome sequence data from a squamous cell carcinoma left mandible and extranodal extension patient

  Genome and transcriptome sequence data from a squamous cell carcinoma left mandible and extranodal extension patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016128

• Genome and transcriptome sequence data from a keratinizing squamous cell carcinoma patient

  Genome and transcriptome sequence data from a keratinizing squamous cell carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016131

• Genome and transcriptome sequence data from a rectal adenocarcinoma patient

  Genome and transcriptome sequence data from a rectal adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016151

• WGS files for paper titled "Sensitive detection of MYCN amplified neuroblastoma in blood samples with structural variants using whole genome sequencing"

  This dataset contains one long read whole genome sequence tumor sample. 2.5µg of patient DNA was used to prepare SMRTbell sequencing library following the “Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0” protocol (PacBio). Sequencing was conducted on PacBio Revio+SPRQ chemistry with 250pM loading concentration, generating 35x mean coverage for the whole genome. Reads were mapped to human genome assembly GRCh37 using pbmm2 v1.17.0 (https://github.com/PacificBiosciences/pbmm2)

  Dataset EGAD00001016133

• CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Angioleiomyoma_WES

  Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

  Dataset EGAD00001016134

• CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Glomus tumour_WES

  Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

  Dataset EGAD00001016135

• CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Angioleiomyoma_RNAseq

  Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

  Dataset EGAD00001016136

• CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Myopericytoma_RNAseq

  Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

  Dataset EGAD00001016137

• Genome and transcriptome sequence data from a esophageal adenocarcinoma patient

  Genome and transcriptome sequence data from a esophageal adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016152

• CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Glomus tumour_RNAseq

  Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

  Dataset EGAD00001016138

• CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Myopericytoma_WES

  Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

  Dataset EGAD00001016139

• Genome and transcriptome sequence data from a adenocarcinoma, non-small cell lung cancer patient

  Genome and transcriptome sequence data from a adenocarcinoma, non-small cell lung cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016149

• Genome and transcriptome sequence data from a adenocarcinoma of the duodenum patient

  Genome and transcriptome sequence data from a adenocarcinoma of the duodenum patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016150

• snRNA sequencing of high-grade pancreatic neuroendocrine carcinoma (panNEC)

  High-grade pancreatic neuroendocrine carcinoma (panNEC) is a rare, aggressive cancer with limited tissue availability. Single-nucleus transcriptomics of five large-cell panNECs revealed two interesting neuroendocrine cell states: one highly proliferative with an aberrant brain-specific neuronal differentiation program and another stress-responsive state enriched for heat stress, hypoxia, and glycolysis. Our findings suggest potential therapeutic vulnerabilities, highlighting the need to evaluate the efficacy of combination therapies.

  Dataset EGAD00001016154

• GBM-Space: Whole Genome Sequencing of Laser Capture Microdissected Glioblastoma (LCM-WGS)

  Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This dataset contains whole genome sequencing (WGS) data generated from regions of interest (ROIs) collected via laser capture microdissection (LCM), towards identifying copy number alterations and subclones directly at the DNA level.

  Dataset EGAD00001016155

• Genome and transcriptome sequence data from a metastatic breast carcinoma patient

  Genome and transcriptome sequence data from a metastatic breast carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016179

• Genome and transcriptome sequence data from a metastatic breast carcinoma patient

  Genome and transcriptome sequence data from a metastatic breast carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016181

• Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

  Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016183

• Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

  Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016184

• Genome and transcriptome sequence data from a metastatic adenocarcinoma of the sigmoid colon patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of the sigmoid colon patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016190

• Genome and transcriptome sequence data from a metastatic melanoma patient

  Genome and transcriptome sequence data from a metastatic melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016194

• Genome and transcriptome sequence data from a pancreatic ductal adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic ductal adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016195

• Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016196

• Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016197

• Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016200

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016201

• Genome and transcriptome sequence data from a sigmoid adenocarcinoma patient

  Genome and transcriptome sequence data from a sigmoid adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016213

• Genome and transcriptome sequence data from a adenocarcinoma of the esophagus patient

  Genome and transcriptome sequence data from a adenocarcinoma of the esophagus patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016216

• Genome and transcriptome sequence data from a leiomyosarcoma patient

  Genome and transcriptome sequence data from a leiomyosarcoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016234

• Genome and transcriptome sequence data from a desmoplastic small round cell sarcoma patient

  Genome and transcriptome sequence data from a desmoplastic small round cell sarcoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016243

• Genome and transcriptome sequence data from a carcinoma ex pleomorphic adenoma recurrent patient

  Genome and transcriptome sequence data from a carcinoma ex pleomorphic adenoma recurrent patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016318

• Genome and transcriptome sequence data from a grade 4 astrocytoma, recurrent patient

  Genome and transcriptome sequence data from a grade 4 astrocytoma, recurrent patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016354

• Genome and transcriptome sequence data from a metastatic rectal carcinoma patient

  Genome and transcriptome sequence data from a metastatic rectal carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016371

• Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016389

• Genome and transcriptome sequence data from a metastatic endometrial stromal sarcoma patient

  Genome and transcriptome sequence data from a metastatic endometrial stromal sarcoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016352

• Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016353

• Genome and transcriptome sequence data from a metastatic low-grade serous carcinoma of ovarian origin patient

  Genome and transcriptome sequence data from a metastatic low-grade serous carcinoma of ovarian origin patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016357

• Genome and transcriptome sequence data from a advanced endometrioid carcinoma (primary unknown) patient

  Genome and transcriptome sequence data from a advanced endometrioid carcinoma (primary unknown) patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015938

• Genome and transcriptome sequence data from a metastatic melanoma patient

  Genome and transcriptome sequence data from a metastatic melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015939

• Genome and transcriptome sequence data from a invasive metastatic adenocarcinoma, originating from extramammary paget’s disease patient

  Genome and transcriptome sequence data from a invasive metastatic adenocarcinoma, originating from extramammary paget’s disease patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015940

• Genome and transcriptome sequence data from a histiocytic sarcoma patient

  Genome and transcriptome sequence data from a histiocytic sarcoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015945

• Genome and transcriptome sequence data from a astrocytoma li fraumeni syndrome patient

  Genome and transcriptome sequence data from a astrocytoma li fraumeni syndrome patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015946

• Genome and transcriptome sequence data from a metastatic melanoma patient

  Genome and transcriptome sequence data from a metastatic melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015948

• Genome and transcriptome sequence data from a osteosarcoma patient

  Genome and transcriptome sequence data from a osteosarcoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015951

• Genome and transcriptome sequence data from a thymoma patient

  Genome and transcriptome sequence data from a thymoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015952

• Genome and transcriptome sequence data from a renal cell carcinoma, non-clear cell patient

  Genome and transcriptome sequence data from a renal cell carcinoma, non-clear cell patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015953