9295 results for "cancer rna-seq"

in 41.31 milliseconds.

• Comprehensive Epigenetic Landscape of Rheumatoid Arthritis Fibroblast-Like Synoviocytes

  We characterized the epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes (FLS) compared with osteoarthritis FLS. Multiple technologies were used, including ChIP-seq to assay H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3, ATAC-seq for chromatin accessibility, the transcriptome by RNA-seq and whole genomic bisulfite sequencing for DNA methylation. Integrative analysis was performed using a novel unbiased method to identify regions of the genome that have similar epigenetic marks. The regions that distinguished RA and osteoarthritis cells were primarily located in active enhancers and promoters. The regions and genes identified included immunological pathways. In addition, some unexpected pathways, most notably "Huntington's Disease Signaling", were discovered. The Huntington's Disease pathway was biologically validated for Huntingtin-interacting protein-1, which regulated invasive behavior of FLS. For a complete description, see R. Ai et al., Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes. Nat Commun 9, 1921 (2018). Sequencing data of study participants are available through dbGaP's Authorized Access portal, while analyses of the sequencing data may be obtained through NCBI's GEO portal under GSE112658.

  Study phs001615

• Sequencing data for "Replication timing alterations are associated with mutation acquisition during tumour evolution in breast and lung cancer"

  Repli-seq data for "Replication timing alterations are associated with mutation acquisition during tumour evolution in breast and lung cancer"

  Dataset EGAD00001015363

• Epithelioid haemangioendothelioma (EHE) case series from the Stafford Fox Rare Cancer Program

  Nine EHE cases with comprehensive histologic and molecular profiling from the Walter and Eliza Hall Institute of Medical Research Stafford Fox Rare Cancer Program were collated via nation-wide referral to the Australian Rare Cancer Portal. Molecular analysis of RNA, DNA or both was possible in seven of nine cases. Survival was highly variable and unrelated to molecular profile. DNA sequences for two cases are deposited here.

  Study EGAS00001007474

• atrial appendage RNA-seq in non-, paroxysmal and persistent atrial fibrillation

  64 left atrial appendages from patients without atrial fibrillation (AF) undergoing cardiac surgery, patients with paroxysmal AF and with persistent AF (~20 per group). Trizol RNA isolation, rRNA depletion, paired transcriptome sequencing on illumina NovaSeq 6000. Provided are FastQ and BAM files. Additional data (e.g. clinical characteristics, RIN values etc.) can be provided upon reasonable request. The same RNA samples (62 out of 64) were used for miRNA sequencing. Results from miRNA seuqencing are stored in the EGA database managed by the same DAC.

  Dataset EGAD00001007693

• RNA and ChIP Sequencing datasets from the study Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma

  This dataset contains the RNA and ChIP Sequencing data from the study Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma. The data is organized in 7 experiments which are divided by both sequencing technology or the application of siRNA or drug interventions (or lack thereof) on neuroblastoma cell lines. The experiment names and the file names have been chosen in each respective experiment to guide future users of the data to replicate the analyses in the manuscript.

  Dataset EGAD00001006964

• atrial appendage miRNA-seq in non-, paroxysmal and persistent atrial fibrillation

  64 left atrial appendages from patients without atrial fibrillation (AF) undergoing cardiac surgery, patients with paroxysmal AF and with persistent AF (~20 per group). Trizol RNA isolation, size selection, single end miRNA sequencing on 4 lanes of illumina NextSeq 500. Provided are FastQ files, one per lane per sample. Additional data (e.g. clinical characteristics, RIN values etc.) can be provided upon request. The same RNA samples (62) were used for transcriptome sequencing. Results from transcriptome sequencing are stored in the EGA database and are managed by the same DAC.

  Dataset EGAD00001007694

• RNA-seq of Toxoplasma gondii response in human macrophages

  Toxoplasmosis is a zoonotic disease caused by a ubiquitous protozoan parasite called Toxoplasma gondii, which can infect all mammal and bird species throughout the world. seroprevalence varies widely between countries. Studies have estimated that between 7-34% of people in the UK have been infected with T. gondii. The vast majority of these people will not have noticed any symptoms, however about 10% of people develop a mild to moderate self limiting flu-like illness. Following the acute active stage of the infection the parasite persists in the body in the form of cysts, particularly in heart and skeletal muscle and nervous system tissues, for many years, and usually for life. In immunocompetent persons these cysts do not pose a health risk. We will use RNA-seq to quantify the transcriptional response of macrophages to T gondii infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001003241

• An Integrated Approach to Patient Stratification and Therapy Selection in Acute Myeloid Leukemia

  As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we developed and validated a clinical transcriptome-based assay for stratification of acute myeloid leukemia (AML). Comparison of RNA-Seq to whole genome and exome sequencing revealed that as a standalone assay, RNA-Seq offered the greatest diagnostic return, enabling identification of expressed gene fusions, single nucleotide and short insertion/deletion variants, and whole-transcriptome expression information. Expression data were used to develop a novel risk score which, when combined with molecular risk guidelines, allowed for the re-stratification of 22.1 to 25.3% of AML patients from three independent cohorts into correct risk groups. Within the adverse-risk subgroup, we identified a subset of patients characterized by dysregulated integrin signaling and RUNX1 or TP53 mutation. We show that these patients may benefit from therapy with inhibitors of focal adhesion kinase (PTK2), demonstrating additional utility of transcriptome-based testing for therapy selection in myeloid malignancy.

  Dataset EGAD00001006701

• The single plasma-cell transcriptional landscape in POEMS syndrome

  POEMS syndrome is a rare monoclonal plasma cell disorder that shows unique symptoms distinct from other plasma cell neoplasms, including high levels of serum VEGF; however, none of the previous studies have succeeded in direct identification of plasma cell clones in POEMS syndrome, leaving their real nature obscure.���We herein performed single-cell RNA sequencing (scRNA-Seq) of bone marrow (BM) plasma cells from patients with POEMS syndrome. These data unveil unique features of POEMS clones among plasma cell neoplasms and enhance our understanding of the pathogenesis of POEMS syndrome.

  Study JGAS000289

• Identification_of_immune_mechanisms_associated_with_the_high_rate_of_relapse_in_patient_with_visceral_leishmaniasis_and_HIV_co_infection

  RNA-seq transcriptomics of whole blood samples from longitudinal follow-up of a cohort of visceral leishmaniasis (VL) patients with and without HIV coinfection, from active disease through apparent cure and potential relapse. Analysis will identify potential correlates of relapse to identify immune mechanisms underlying the high rate of relapse in HIV/VL coinfection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001003465