12302 results for "cancer rna-seq"

in 29.67 milliseconds.

• SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors

  Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we studied derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids revealed a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently revealed patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 drives patient-specific epigenetic reprogramming underlying MRT tumorigenesis.

  Study EGAS00001007590

• RNA-Seq-Dataset

  RNA-Seq-Dataset

  Dataset EGAD00001000043

• RNA-seq data for study 'Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk.'

  RNA-seq data from nasal and bronchial tissues in 649 subjects, many with lung cancer. Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to lifestyle risk in the form of cigarette smoke has long been established. More than 50% of all smoking-related lung cancers occur in former smokers, often many years after smoking cessation. Despite extensive research, the molecular processes for persistent lung cancer risk are unclear. CT screening of current and former smokers has been shown to reduce lung cancer mortality by up to 26%. To examine whether clinical risk stratification can be improved upon by the addition of genetic data, and to explore the mechanisms of the persisting risk in former smokers, we have analyzed transcriptomic data from accessible airway tissues of 487 subjects. We developed a model to assess smoking associated gene expression changes and their reversibility after smoking is stopped, in both healthy subjects and clinic patients. We find persistent smoking associated immune alterations to be a hallmark of the clinic patients. Integrating previous GWAS data using a transcriptional network approach, we demonstrate that the same immune and interferon related pathways are strongly enriched for genes linked to known genetic risk factors, demonstrating a causal relationship between immune alteration and lung cancer risk. Finally, we used accessible airway transcriptomic data to derive a non-invasive lung cancer risk classifier. Our results provide initial evidence for germline-mediated personalised smoke injury response and risk in the general population, with potential implications for managing long-term lung cancer incidence and mortality.

  Dataset EGAD50000000333

• glioblastoma and glioblastoma stem cells (GSCs), RNA-seq and WGS

  Characterization of glioblastoma tumors and glioblastoma stem cells (GSCs) lines via RNA-seq and/or WGS profiling.

  Study EGAS00001004395

• Prognostic whole-genome and transcriptome signatures in colorectal cancers

  This dataset consists of RNA-seq CRAM raw-data files of 1063 primary colorectal cancer and 120 adjacent normal tissue samples. The expression profiles for these samples can be found at the ArrayExpress with accession number E-MTAB-12862.

  Dataset EGAD50000000169

• RNA-seq dataset

  HTG EdgeSeq fastq files of bulk baseline tumors from IMbassdor250: a randomised phase 3 trial comparing atezolizumab with enzalutamide vs enzalutamide alone in patients with metastatic castration-resistant prostate cancer.

  Dataset EGAD00001007685

• RNA-seq

  RNA-seq data

  Dataset EGAD00001011376

• Paired Biopsy Project: West Coast Dream Team

  This project aims to analyze the paired metastatic biopsy samples from patients with metastatic castration-resistant prostate cancer (mCRPC), collected before the initiation of the first-line androgen receptor signaling inhibitor (ARSI) for mCRPC and after radiographic disease progression on that ARSI, to understand the resistance mechanisms. We generated both whole genome sequencing (WGS) and RNA-seq data on these samples. A majority of these samples have been deposited in the public domain along with prior publications, and this project contains the 16 WGS samples that have not yet been deposited.

  Study EGAS50000000327

• H3K27ac ChIP-seq and RNA-seq of lung neuroendocrine tumors

  H3K27ac ChIP-seq and RNA-seq of lung neuroendocrine tumors

  Dataset EGAD50000000083

• RNA-seq and ATAC-seq data for ex vivo expanded T cells

  This dataset contains bulk RNA-seq and ATAC-seq data generated from naïve CD8+ T cells isolated from PBMCs of three healthy donors and stimulated ex vivo under multiple conditions. The dataset comprises 30 samples in total, including 15 RNA-seq samples and 15 ATAC-seq samples. Paired-end sequencing was performed on the Illumina NovaSeq 6000 platform. Raw data are provided as gzipped paired FASTQ files.

  Dataset EGAD50000002471