11932 results for "cancer rna-seq"

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• Single-Cell and Bulk RNA Sequencing of Oncolytic Measles Virus Treatment in Pediatric Medulloblastoma and ATRT

  This dataset includes single-cell RNA sequencing profiles from five mice bearing Group 3 medulloblastoma (CSCG) treated with oncolytic measles virus (MV-NIS) and three mice treated with MV-NIS combined with anti-PD1 therapy. Additionally, bulk RNA sequencing data were generated from 12 samples across PBS control, heat-inactivated (HI) control, MV mid-treatment, and treatment resistance conditions. Pediatric patient data were collected from the PNOC005 trial, which enrolled patients into three strata: Stratum A (focal recurrence, local MV-NIS administration post-surgical resection), Stratum B (disseminated recurrence, single MV-NIS dose via lumbar puncture), and Stratum C (disseminated recurrence, two consecutive MV-NIS doses via lumbar puncture on Day 0 and Day 7). Whole blood and PBMC samples were collected from 17 patients across all strata, generating 72 bulk RNA-seq datasets at multiple time points. All datasets are provided as raw sequencing data in FASTQ format.

  Dataset EGAD50000001197

• Sexual dimorphism in human immune system aging

  We isolated peripheral blood mononuclear cells (PBMCs) from 172 community-dwelling healthy volunteers (91 women, 81 men) ages spanning adult lifespan: 54 young (ages 22-40: 23 men, 31 women), 59 middle-aged (ages 41-64: 31 men, 28 women), and 59 older subjects (65+: 27 men, 32 women). PBMCs were profiled using ATAC-seq (54 men, 66 women), RNA-seq (41 men, 34 women), and flow cytometry (62 men, 67 women). Flow cytometry data is publicly available, genomic data for 121 individuals are provided here. These datasets revealed immune system aging signatures in men and women and showed in which ways aging differentially affects the immune systems of men and women. A subset of these samples have been generated and analyzed previously and can be found at EGA (EGAS00001002605). This dataset on dbGaP include EGA samples as well.

  Study phs001934

• Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis

  The role of non-coding variants in polygenic skin disease and their connection to homeostatic transcription factors (TFs) in epidermis was investigated. Homeostatic TFs were identified by perturb-seq in differentiating keratinocytes, using either 10x or split-pool approaches to sequencing, with follow-up validation by siRNA and RNA-seq. TF binding events were profiled by population sampling Cleavage Under Targets & Release Using Nuclease (CUT&RUN), in which a random population of neonatal foreskin keratinocytes were assayed by CUT&RUN for homeostatic TFs under progenitor growth and differentiation conditions. Heterozygous alleles were identified from the TF binding data and examined for allele specific binding events (ASBs). ASBs were then compared with non-coding variants linked to skin disease. Variants with potentially pathogenic effects were identified. Promoters and high TF occupancy genomic regions were found to be "buffered" against variants causing ASBs.

  Study phs003977

• Single cell multi-omic study of H3-K27M mutant diffuse midline glioma across age and location

  Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in childhood diffuse midline gliomas (DMGs) of the pons, but are also increasingly recognized in adult DMGs. Their potential heterogeneity at different ages and midline locations are vastly understudied. Here, through dissecting the single-cell transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We conducted multi-omic profiling of 50 H3-K27M mutant patient tumors. We performed deep full-length Smart-seq2 fresh single-cell (n=18) or frozen single-nucleus (n=25) RNA-sequencing (sc/snRNA-seq) of 43 tumors). We additionally analyzed the open chromatin profiles of 8 tumors utilizing the single-cell/nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)

  Study EGAS00001006994

• Peripheral blood RNA sequencing of samples for a healthy cohort and a cohort with cancer patients

  RNA sequencing (fastq files) of white blood cells (WBCs) from healthy donors (n=376) and cancer patients (n=421) with different diagnoses, stages of disease and previously administered treatments, was performed. Samples from cancer patients were collected from the BostonGene clinical program; all patients provided written consent per IRB-approved protocols. Blood samples from healthy donors were purchased from multiple collection centers throughout the United States. Whole blood samples (3 ml) in K2-EDTA tubes received within 24 hours of collection at RT underwent red blood cell (RBC) lysis to isolate WBCs. Isolated WBCs for RNA sequencing were centrifuged at 300 x g for 5 minutes with a maximum of 10^6 cells per vial. The supernatant was removed, and the cells were resuspended in cold Homogenization Buffer (2% 1-Thioglycerol, Promega). Samples were then frozen at -80°C until extraction. RNA extraction was performed from frozen samples with Maxwell RSC simplyRNA Cells Kit (Promega) using the benchtop automated Maxwell RSC Instrument (Promega). Libraries were prepared with Illumina TruSeq® Stranded mRNA Library Prep (Poly-A mRNA; stranded). Libraries were sequenced on NovaSeq 6000 as Paired-End Reads (2x150) with targeted coverage of 50 mln reads.

  Dataset EGAD50000000414

• Genomics and Epigenomics of the Elderly Response to Pneumococcal Vaccines

  Pneumococcal Vaccine Study: This is a study designed to develop a detailed transcriptional and cellular profile of the immune response to pneumococcal vaccination with conjugated and non-conjugated polysaccharide vaccines in the senescent immune system of older adults. In this study, 39 healthy adults ages 60 and older that have never received pneumococcal vaccination, have been randomized to receive Prevnar 13 (Pfizer), a conjugated 13-valent vaccine or Pneumovax 23 (Merck), a non-conjugated 23-valent vaccine. Four (4) study visits occurred over 70 days at Day -7 (baseline), day 1, day 10 and day 60 (± 5d) post vaccination.Bulk RNA-sequencing data are available on the 4 time points for 31 of the participants and 1 replicate. ATAC-Doublet Detector Study: We generated single nucleus ATAC-seq (snATAC-seq) data from PBMCs of 2 baseline blood samples from the pneumococcal study. Generated data was then used to benchmark a novel computational method for detecting multiplets in snATAC-seq data, namely, AMULET (https://github.com/UcarLab/AMULET). Multiplets confound downstream analyses by introducing combined epigenomic profiles from 2 or more cells/nuclei. AMULET detects multiplets by using unique snATAC-seq data features that allow it to reliably use read counts to detect multiplets for their removal from data analyses.

  Study phs002361

• 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

• 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

• 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

• 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