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Breast cancer single-cell whole genome sequencing: BioProject supporting "Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing"
- Description
Single-cell genome sequencing of breast cancer. Raw sequence reads from 2,040 SRA experiments based on 18 BioSamples. This data was generated for the study "Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing." Published in eLife.
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Breast NeoplasmsWhole Genome Sequencing
- Access Rights
- Free to All
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Listeria seeligeri LS46 and LS59 Genome sequencing and assembly
- Description
BioProject description: "Genome sequencing of Listeria seeligeri LS46 and LS59". The whole genome sequencing of these listeriaphage enabled researchers to discover that AcrVIA1, an anti-CRISPR protein, interacts with the guide-exposed face of Cas13a, a (crRNA)-guided nuclease, preventing access to the target RNA and the conformational changes required for nuclease activation. A single dose of AcrVIA1...
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ListeriaSequence AnalysisWhole Genome Sequencing
- Access Rights
- Free to All
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Dnmt3a regulates myeloproliferation and liver-specific homing and expansion of hematopoietic stem and progenitor cells (Bisulfite-Seq)
- Authors
- Guryanova, OlgaSpitzer, BarbaraGarrett-Bakelman, FrancineLevine, Ross L.
- Description
Summary from GEO: "DNMT3A mutations are observed in myeloid malignancies, including myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), and acute myeloid leukemia (AML). Here we investigated the impact of conditional hematopoietic Dnmt3a loss on disease phenotype in primary mice. Dnmt3a ablation led to a lethal, fully penetrant myeloproliferative neoplasm with myelodysplasia (MDS/MPN)...
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DNA Methyltransferase 3AHematopoiesisHepatomegalyLeukemia, Myeloid, AcuteMyelodysplastic SyndromesTranscriptomeWhole Genome Sequencing
- Access Rights
- Free to All
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CoMMpass IA19: Data from "Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival"
- Description
The Multiple Myeloma Research Foundation (MMRF) runs a multi-site longitudinal clinical registry study of patients newly diagnosed with MM. This project is called CoMMpass, and collects both clinical and genomic information periodically. Researchers used interim analysis 19 (IA19) for their conclusions in "Gene interaction network analysis in multiple myeloma detects complex immune dysregulation...
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Clinical TrialDNA Copy Number VariationsGenomicsMultiple MyelomaRNA-SeqWhole Genome Sequencing
- Access Rights
- Free to all with registration
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Medulloblastoma (PCGP, Nature 2012)
- Description
Whole genome sequencing of 37 medulloblastoma tumors and their matched normals from the Pediatric Cancer Genome Project (PCGP), a joint project by St. Jude Children's Research Hospital and Washington University. The clinical data includes patient demographics, information about survival status, tumor cellularity dominant pathology reviews, and mutation counts. The data set also includes charts visualizing...
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GenomicsMedulloblastomaMutation/geneticsWhole Genome Sequencing
- Access Rights
- Free to All
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Medulloblastoma (DKFZ, Nature 2017)
- Description
Whole genome or whole exome sequencing of 491 previously untreated Medulloblastoma tumor/normal pairs. The clinical data consists of 491 samples from 491 patients, and includes mutation count, structural variants, patient demographics, and tumor subtypes. The data set also includes charts visualizing data summaries and a customizable plotting tool.
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Exome SequencingGenomicsMedulloblastomaMutation/geneticsWhole Genome Sequencing
- Access Rights
- Free to All
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Medulloblastoma (Sickkids, Nature 2016)
- Description
Whole-genome sequencing of 46 recurrent medulloblastoma samples from 46 patients. The clinical data includes patient demographics, structural variants, mutation counts, and a KM plot. The data set also includes charts visualizing data summaries and a customizable plotting tool.
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GenomicsMedulloblastomaMutation/geneticsWhole Genome Sequencing
- Access Rights
- Free to All
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CLL Genome
- Description
Description from EGA: "The Chronic Lymphocytic Leukemia (CLL) Genome Project aims to identify genetic alterations involved in the development and progression of the CLL, which are still unknown, with the objective of generating a comprehensive catalogue of genetic alterations in 500 independent tumours. The CLL Genome Project, as a contributing member of the International Cancer Genome Consortium...
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Leukemia, Lymphocytic, Chronic, B-CellMutation/geneticsRNA Splicing FactorsWhole Genome Sequencing
- Access Rights
- Application Required
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A practical guide for mutational signature analysis in hematological malignancies
- Description
Description from EGA: "Analysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, prognosis, and even treatment decisions. However, the field lacks a consensus on analysis and result interpretation. Using whole-genome sequencing of multiple myeloma (MM), chronic lymphocytic leukemia (CLL) and acute myeloid leukemia, we compare the...
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GenomicsHomologous RecombinationLeukemia, Lymphocytic, Chronic, B-CellMultiple MyelomaWhole Genome Sequencing
- Access Rights
- Application Required
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WGS short read and 10X linked read sequencing of HR Deficient breast cancers
- Description
Description from EGA: "A set of tumor/normal paired sequencing experiments, performed in short read WGS and 10X linked read whole genomes. BAM files aligned to hg19 are provided. Sample Alias number and Subject ID reflects patient of origin. T/N distinction discriminates between tumor and normal (peripheral blood) tissue."
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Breast NeoplasmsHomologous RecombinationWhole Genome Sequencing
- Access Rights
- Application Required