4859 results for "*oma"

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• Orthotopic murine Group 3 medulloblastoma in C57Bl/6 mice treated with saline, cyclophosphamide or gemcitabine

  Mice with medulloblastoma (Group 3) were treated with saline, cyclophosphamide, or gemcitabine as described by Abbas et al (2020). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen), library preparation (SureSelect, Agilent), rRNA depletion (Ribo-Zero Plus, Illumina) and sequencing were carried out by GenomicsWA or Australian Genome Research Facility. Libraries were sequenced on NovaSeq 6000 S1 flow cells as paired-end 150bp reads (Illumina).

  Dataset EGAD00001008511

• Targeted sequencing of diffuse large B-cell lymphoma tumour samples from the UK's Haematological Malignancy Research Network

  Targeted sequencing was applied to an unselected population-based diffuse large B-cell lymphoma cohort (n=928) diagnosed in the UK's Haematological Malignancy Research Network catchment population of ~4 million (14 centres). DNA extracted from tumour samples was sequenced with a 293-gene panel using the Illumina HiSeq 2500. All data are provided in the CRAM format.

  Dataset EGAD00001008616

• Whole genome, exome and RNA sequencing of TFCP2-rearranged rhabdomyosarcoma

  Whole genome, exome and RNA sequencing of TFCP2-rearranged rhabdomyosarcoma, 86 samples of paired fastq files, sequenced on: Illumina HiSeq 2500 using Agilent SureSelect WGS, Illumina HiSeq 2500 using Illumina TruSeq RNA, Illumina HiSeq 2500 using Agilent SureSelect v5 WES (+UTRs), Illumina HiSeq 4000 using Agilent SureSelect WGS, Illumina HiSeq 4000 using Illumina TruSeq stranded mRNA Kit, Illumina HiSeq 4000 using Agilent SureSelect v5 WES stranded mRNA Kit, Illumina NovaSeq 6000 using Illumina TruSeq Stranded mRNA, Illumina NovaSeq 6000 using Illumina TruSeq Nano DNA, Illumina HiSeq X Ten using TruSeq Nano DNA.

  Dataset EGAD00001010108

• Genome and transcriptome sequence data from a ductal carcinoma of left breast patient

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

  Dataset EGAD00001002574

• Genome and transcriptome sequence data from a diffuse intrinsic pontine glioma tumor patient

  Genome and transcriptome sequence data from a diffuse Intrinsic Pontine Glioma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015284

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

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

  Dataset EGAD00001002589

• Genome and transcriptome sequence data from a myxoid liposarcoma patient

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

  Dataset EGAD00001002620

• Genome and transcriptome sequence data from an endometrial carcinoma patient

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

  Dataset EGAD00001002633

• Genome and transcriptome sequence data from a ewing sarcoma tumor patient

  Genome and transcriptome sequence data from a ewing sarcoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015286

• Clear cell sarcoma dataset

  This deposit consists of DNA and RNA sequencing data from 67 CCS samples. 55 samples had tumor DNA sequencing data. 6 had matched normal sequencing data. 34 samples had tumor RNA sequencing data.

  Dataset EGAD00001008611

• Single-cell mRNA-sequencing to generate a transcriptomic atlas of RMS

  Single-cell mRNA-sequencing to generate a transcriptomic atlas of soft tissue sarcoma tumors

  Dataset EGAD00001009385

• Differential methylation positions

  This dataset includes an analyzed DMP file that provide the information about differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. Of the five lung cancer cases, 3 are adenocarcinoma and 2 are squamous carcinoma.

  Dataset EGAD00001010147

• Genome and transcriptome sequence data from a NUT midline carcinoma tumor patient

  Genome and transcriptome sequence data from a NUT midline carcinoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015289

• RNA-Seq data on multiple myeloma CD138positive bone marrow plasma cells

  RNA-Seq data on multiple myeloma CD138positive bone marrow plasma cells, 11 samples, sequenced on HiSeq 4000 and HiSeq X-Ten, using mostly the TruSeq stranded mRNA Kit.

  Dataset EGAD00001008619

• Genome and transcriptome sequence data from a minimally invasive adenocarcinoma tumor patient

  Genome and transcriptome sequence data from a minimally invasive adenocarcinoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015297

• Whole genome sequencing of Multiple Myeloma CD138positive bone marrow plasma cells and saliva control samples

  Whole genome paired sequencing of Multiple Myeloma CD138positive bone marrow plasma cells and saliva control samples (6 tripletts, tumor1, tumor2, saliva control) from 6 patients. WGS was done on HiSeq X-Ten or Novaseq 6000 with Illumina TruSeq Nano DNA.

  Dataset EGAD00001008618

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

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

  Dataset EGAD00001010950

• Genome and transcriptome sequence data from a unknown primary adenocarcinoma patient

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

  Dataset EGAD00001010953

• Merged single-cell RNA-seq data for 22 Hodgkin lymphomas and 5 reactive lymph nodes

  This dataset contains merged data from the 22 Hodgkin lymphoma and 5 reactive lymph node samples, including count data and cell cluster assignments.

  Dataset EGAD00001006221

• 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 EGAD00001010965

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

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

  Dataset EGAD00001010977

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

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

  Dataset EGAD00001010996

• 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 EGAD00001011004

• Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild type primary glioblastoma

  We stratified 69 primary IDH-wt GBM patients into TMZ-resistant (n = 29) and sensitive (n = 40) groups, using TMZ screening of the corresponding patient-derived glioma stem-like cells (GSCs). Genomic and transcriptomic features were then examined to identify TMZ-associated molecular alterations. Subsequently, we developed a machine learning (ML) model to predict TMZ response from combined signatures. Moreover, TMZ response in multisector samples (52 tumor sectors from 18 cases) was evaluated to validate findings and investigate the impact of intra-tumoral heterogeneity on TMZ efficacy.

  Dataset EGAD00001010156

• Prognostic relevance of microenvironmental factors CD163 and CD8 combined with EZH2 and chromosome 18 gain in a validation cohort of follicular lymphoma patients of the Lunenburg Lymphoma Biomarker Consortium

  Background: In follicular lymphoma (FL), studies addressing the prognostic value of microenvironment-related immunohistochemical (IHC) markers and tumor cell-related genetic markers have yielded conflicting results, precluding implementation in practice. Therefore, the Lunenburg Lymphoma Biomarker Consortium (LLBC) performed a validation study for published markers. Methods: To maximize sensitivity, an end-of-spectrum design was applied for 122 uniformly immunochemotherapy-treated FL patients retrieved from international trials and registries; early failure (EF): progression or lymphoma-related death <2 years versus long remission: response duration of >5 years. IHC staining for T-cells and macrophages was performed on tissue microarrays from initial biopsy and scored with a validated computer-assisted protocol. Shallow whole-genome and deep targeted sequencing was performed on the same samples. Results: 96/122 cases with complete molecular and immunohistochemical data were included in the analysis. EZH2 wild-type (p=0.006), gain of chromosome 18 (p=0.002), low percentages of CD8+ cells (p=0.011) and CD163+ areas (p=0.038) were associated with EF. No significant differences in other markers were observed, thereby refuting previous claims on their prognostic significance. Conclusion: Using an optimized study design, this LLBC study validates wild-type EZH2 status, gain of chromosome 18, low percentages of CD8+ cells and CD163+ area as predictors of EF to immunochemotherapy in FL.

  Dataset EGAD00001002738