9295 results for "cancer rna-seq"

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• scRNA-seq and scTCR-seq data IMCISION

  We performed single cell RNA and TCR sequencing (10x Genomics) on immune infiltrates (CD45+ cells) from 18 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021). Viable immune cells were isolated from pre-treatment and on-treatment primary tumor biopsies of 10 patients responding (1 partial pathological response and 9 major pathological responses) and 7 patients non-responding to anti-PD-1 and anti-CTLA4 combination immunotherapy. One patient treated with anti-PD-1 monotherapy (1 major pathological response) was included in the dataset.

  Study EGAS00001007368

• Y90 radioembolization followed by intravenous Nivolumab for advanced hepatocellular carcinoma

  To evaluate the efficacy of combination therapy with ICI and RT in patients, a Phase II trial (CA209-678) was conducted to investigate the efficacy and safety of Y90-RE followed by nivolumab in patients with advanced HCC (NCT03033446, n = 36). Interestingly, the ORR was found to be 30.6% in all patients and 43.5% when restricted to patients with only intrahepatic tumors, suggesting possible synergism between Y90-RE and ICI. Here we present whole exome sequencing (WES) and RNA-seq data for 33 patients treated with Y90 radioembolization followed with Nivolumab.

  Study EGAS00001006834

• Genetic and Epigenetic Determinants of Pediatric Obesity-Associated Asthma

  Fifty-nine obese and sixty-one normal-weight asthmatic children of African American or Hispanic background, age 7-11 years, with well controlled asthma, were recruited from clinics affiliated with Children's Hospital at Montefiore, Bronx, New York, USA. We isolated CD4+ T cells (Th cells) from a fasting sample of peripheral blood and conducted genome-wide assays of gene expression by Directional Transcriptome Sequencing (RNA-seq), DNA methylation by HELP-tagging, and examined genetic polymorphisms and single nucleotide polymorphisms (SNPs), informative about ancestry, by array-based genotyping using Multi-Ethnic Genotyping Array.

  Study phs001812

• Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

  This observational study was designed to determine the cellular tropism of Influenza A and B Viruses (IAV, IBV) from samples taken from the upper respiratory tract collected during routine nasal washes during the 2017-2018 season. Using single-cell RNA sequencing (scRNA-seq) we sought to determine which cell types could be infected, what the cellular response was to infection in both infected and bystander cells, and to compare the intra/inter-host variability of IAV and IBV during a single season at a single healthcare provider location.

  Study phs002039

• Avelumab or M7824 for People with Recurrent Respiratory Papillomatosis

  This submission includes genomic data derived from the study of clinical samples from two different phase II trials. These trials evaluated the clinical efficacy and safety of avelumab or M7824 in the treatment of adults with recurrent respiratory papillomatosis (RRP). Subjects with aggressive RRP were treated with three to six doses of avelumab or M7824. Pre-treatment or post-treatment snap frozen papilloma and normal mucosa samples were subjected to whole exome sequencing and bulk RNA-seq. A total of twenty subjects were enrolled and treated. 

  Study phs002373

• Novel Approach to High-Throughput Identification and Characterization of Neoantigens

  This study focuses on the development of novel approach for the screening, identification and characterization of neoantigen-specific T-cell receptors (TCRs). The developed method consists of collecting targeted RNA-Seq from a T-cell specific gene panel via 3' end Illumina sequencing combined to Oxford Nanopore based full-length TCR sequencing post T-cell activation. The data generated during this study demonstrates feasibility of the approach on a Jurkat control cell line as well as T-cells isolated from the blood of 3 independent healthy donors.

  Study phs002372

• Leveraging Extended Families for Cardiovascular Disease Genomic Discovery

  This study characterizes a large early onset atrial fibrillation family and identifies a rare causative mutation (R231H) in the KCNQ1 gene. The age of this mutation is ~5000 years, as estimated using IBD-coalescent methods. The geographic distribution and demographic history of the mutation is described. Induced pluripotent stem cell derived cardiomyocytes carrying the mutation have abbreviated action potential duration, indicating a gain-of-function. This data resource provides exome or whole genome sequencing data for six patients and RNA-seq data from the cardiomyocyte experiments. 

  Study phs002464

• Multi-Omic Investigation of Beckwith-Wiedemann Syndrome Wilms Tumor

  Wilms’ Tumor (WT), also known as nephroblastoma, is one of the most common malignant kidney tumors diagnosed in children. One of the most common WT predisposition syndromes is Beckwith-Wiedemann Syndrome (BWS, OMIM: 130650), which affects approximately 1/10,000 live births. In this study, we perform Whole Exome Sequencing (WES), DNA methylation array, and messenger RNA-Sequencing (mRNA-Seq), to examine the genomic, methylomic, and transcriptomic signature of BWS WT. We analyzed six tumor-normal paired samples, three BWS tumor only samples, and four non-BWS control samples to identify BWS WT drivers.

  Study phs002769

• Single Nucleus Transcriptomes from the Ventral Midbrain of Opioid Overdose Cases and Controls

  We generated ventral midbrain single nuclei RNA-seq libraries for 95 brain donors, including 45 subjects with documented histories of opioid abuse and overdose, and 50 demographically-matched, opioid-free control subjects, collected from two geographically distinct regions within the U.S. (greater Detroit area, Michigan and Miami, Florida). Each sample included both substantia nigra and the adjacent ventral tegmental area. Nuclei were processed in pools of 3-4 brains using the 10X Chromium system followed by Illumina sequencing, read alignment and processing by 10X Cellranger.

  Study phs003260

• Protracted Neuronal Recruitment in the Temporal Lobe of Young Children

  This study describes a stream of migrating neurons directed to the human entorhinal cortex. This migration is among the most protracted in the developing human brain, with young neurons still arriving at 2-3 years of age. We did not observe a similar migratory process in the early postnatal macaque brain, which suggests that this migration may be uniquely delayed or extended into early postnatal human life. Using immunohistochemistry and single‐cell RNA sequencing (scRNA‐seq), we identified these late-arriving neurons as being mainly CGE-derived LAMP5+/RELN+ interneurons.

  Study phs003509