13384 results for ""60+mice"+"6+weeks"+diet+study+2014+2017+DOI"

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• Transcriptome analysis of leiomyosarcoma

  We performed transcriptome analysis of leiomyosarcoma

  Study EGAS50000000594

• Transcriptomic profiling of prostate cancer metastasis xenograft models reveals conservation of bone microenvironment signatures

  Study EGAS00001004770

• BIOCLOCK Study Methylation Data

  Whole blood methylation data measured using Illumina MethylationEPIC v2.0 array

  Dataset EGAD00010002801

• Epigenetic reprogramming shapes monocytes and heterologous T cell derived cytokine responses in BCG vaccination

  Study EGAS00001007498

• Homologous recombination DNA repair deficiency and activity of PARP inhibition in primary triple negative breast cancer

  Study EGAS00001004190

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus

  Study EGAS00001003679

• Altered neutrophil and granulopoiesis biology underlie a poor outcome sepsis endotype

  Study EGAS00001006283

• Multi-modal analysis of pediatric pilocytic astrocytomas reveals tumor location-associated cellular and transcriptional heterogeneity

  Study EGAS00001008187

• Oncolytic virotherapy mediated anti-tumor response in primary cutaneous B-cell lymphoma: a single-cell perspective

  Study EGAS00001004904

• Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor infiltrating T cells.

  Study EGAS00001006141

• IG-MYC rearrangement defines a high-risk subgroup of B-cell precursor acute lymphoblastic leukaemia

  Study EGAS00001005111

• Anaplastic_Meningioma_V3__cancer_gene_panel

  Investigation into causal genes underlying anaplastic meningioma

  Study EGAS00001001155

• RNA-seq PE

  Transcriptomics of paired-end RNA-seq data

  Study EGAS00001006522

• Bulk RNAseq of mCRC organoids

  Transcriptomic profiles of 6 mCRC organoids

  Study EGAS00001006727

• Second hit rare genetic variants in families with seemingly GBA gene associated Parkinson’s disease

  Study EGAS00001004777

• RNA-seq SE

  Transcriptomics of single-end RNA-seq data

  Study EGAS00001006521

• Genomic Sequencing of Triple Negative Breast Cancer - CUTseq data

  CUTseq data for study EGAS00001008261

  Dataset EGAD00001015684

• Effects of interferon-gamma treatment on human small intestinal organoids generated from healthy donors

  The intestine is vulnerable to interferon-gamma as intestinal epithelial stem cells undergo cell death when exposed to interferon-gamma. Here, we developed a novel human intestinal organoid-based 3D model system to study the effects of interferon-gamma-induced intestinal epithelial damage at the RNA level. We treated organoids with 10 ng/mL for either 6 or 18h. Knowledge generated with this dataset is relevant for a variaty of intestinal pathologies with an immune component, for instance graft-versus-host disease.

  Study EGAS50000000083

• Characterizing Disease-Causing Variants Using Personal Genomes with Large Recurrent Deletions

  Individuals with recurrent genomic deletions are known to present variable clinical phenotypes, despite the apparent identical range of the genomic segments being affected in their genomes. We propose to study the phenotypic variability and the molecular polymorphism in individuals with the recurrent 17q12 deletions or the recurrent 1q21.1 deletions, with the objective to establish causal relationship between the genotypes and the incompletely penetrant clinical phenotypes. Genome sequencing and phenotypic data from individuals with the deletions and their relatives are included in this submission.

  Study phs002613

• Comprehensive Analysis of Structural Variants in Breast Cancer Genomes Using Single Molecule Sequencing

  This study used the SKBR3 breast cell line and tumor/normal organoids derived from breast tissue to explore the utility of long read sequencing for detecting structural variants in complex samples. Three technologies were used to characterize the samples: Illumina/10X, Pacific Biosciences, and Oxford Nanopore. Methylation results were derived from the Oxford Nanopore data. It is hoped that this resource will better help researchers better understand the utility of long read sequencing in cancer samples.

  Study phs002210

• Enrichment of PTPRT and JAK2 mutations in lung cancer from African Americans and evidence for increased GI and HRD in LUSC

  The goal of this study is to compare the somatic mutation landscape between European Americans and African Americans. It includes various histological forms of lung cancer. In LUAD, we find increased prevalence of PTPRT and JAK2 mutations among African Americans. These proteins function in the same pathway and as such, this may be a new actionable target for lung cancer. We have also examined the landscape of copy number profiles in African Americans and European Americans.

  Study phs001895

• Pharmacogenomics of Mercaptopurine Intolerance in Children with Acute Lymphoblastic Leukemia (AALL03N1)

  Mercaptopurine (MP) is the mainstay of curative therapy for acute lymphoblastic leukemia (ALL). We performed a genome-wide association study (GWAS) to comprehensively identify the genetic basis of MP intolerance in children with ALL in AALL03N1. MP dose intensity was defined as prescribed dose divided by the planned protocol dose during maintenance therapy.  Germline variants in NUDT15 and TPMT were found to be strongly associated with MP intolerance in childhood ALL, which may have implications for treatment individualization in this disease.

  Study phs002846

• DNA and RNA Profiling Using Simultaneous Sequencing (Simul-seq)

  Paired DNA and RNA profiling is increasingly employed in genomics research to uncover molecular mechanisms of disease and to explore personal genotype and phenotype correlations. We developed a novel simultaneous DNA and RNA sequencing approach (Simul-seq) that enables comprehensive genomic and transcriptomic profiles from small quantities of cells or tissues. In this study, Simul-seq was performed on patient-derived fibroblast cells as well as an esophageal adenocarcinoma tumor sample and compared with standard DNA and RNA-sequencing approaches.

  Study phs001214

• Circulating Tumor DNA Sequencing Provides Comprehensive Mutation Profiling for Pediatric Central Nervous System Tumors

  Tumor molecular profiling is increasingly important for the diagnosis and clinical management of childhood brain tumors, including diffuse midline glioma (DMG). We established a targeted deep sequencing approach using the TruSight Oncology 500 ctDNA exome panel to detect tumor genomic mutations and copy number variations in circulating tumor DNA from children diagnosed with DMG. In this study, we present the sensitivity, specificity, and clinical implications of our liquid biopsy sequencing approach for tumor genome profiling in children with DMG.

  Study phs003022

• Small Genomic Insertions Form Enhancers that Misregulate Oncogenes

  ChIP-Seq data from 102 cell lines were processed to identify insertions relative to the human reference genome. To confirm the ability of a computational pipeline to identify insertions that are actually present in these genomes, we PCR-amplified and deeply sequenced regions where insertions were predicted to exist in MOLT4 T-cell acute lymphoblastic leukemia cells. The current study release makes available sequences of amplicons from a tumor cell genome (MOLT4) where a computational pipeline predicted small insertions from orthogonal data.

  Study phs001242