11762 results for "cancer rna-seq"

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• BLUEPRINT release January 2015, RNA-Seq for common lymphoid progenitor

  RNA-Seq data for 5 common lymphoid progenitor sample(s). 20 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001184

• The effect of anti-HER2/CD3 TDB on transcription in human PBMCs (single-cell RNA-seq)

  Single-cell RNA-seq libraries were generated from human PBMCs that were incubated with anti-HER2/CD3 TDB in the presence of KPL-4 cells. This dataset is linked with the following ArrayExpress Experiment: E-MTAB-8212 - The effect of anti-HER2/CD3 TDB on transcription in human PBMCs (single-cell)

  Dataset EGAD00001005188

• Illumina RNA-Seq paired of 10 different tumor samples from the Master program (H021)

  Fastq files of paired RNA-Seq of 10 different tumor samples, for which Nanopore and Illumina sequencing was compared. Illumina sequencing was carried out with HiSeq4000 or HiSeq X-Ten using the Illumina TruSeq stranded mRNA Kit.

  Dataset EGAD00001008971

• Paired RNA-Seq data of 65 samples of chemo-naïve and post-chemotherapy pancreatic ductal adenocarcinoma (PDAC)

  130 runs/ 65 samples of paired RNA-Seq data of chemo-naïve and post-chemotherapy pancreatic ductal adenocarcinoma (PDAC). The sequencing was done on Novaseq 6000 with Illumina TruSeq stranded mRNA Kit.

  Dataset EGAD00001010883

• RNA-seq dataset: Short-term fasting before living kidney donation has an immune-modulatory effect

  This dataset contains 13 RNA-seq samples in CRAM format, generated using the Illumina NovaSeq 6000 platform. The Roche_mRNA_UniversalAdapterUniquePrime protocol was used for library preparation. The aim of the study is to determine the effect of Short-Term Fasting on the abundance and phenotype of different immune cell populations.

  Dataset EGAD00001015472

• Genomic, transcriptomic and epigenomic profiling of GCTB

  Giant cell tumor of bone is a rare bone neoplasm driven by oncogenic hotspot G34W/L/V mutations in the non-canonical histone variant H3.3. This study provides primary data of genomic (WGS), transcriptomic (RNA-seq) and epigenomic (histone mark ChIP-seq, WGBS, ATAC-seq) profiling of primary GCTB samples from several cohorts in Germany and Korea. We confirm the H3.3-G34 mutations as sole genetic drivers of GCTB, and describe the epigenetic alterations in mutant GCTB stromal cells.

  Study EGAS00001003730

• Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma, lung and colon cancer samples

  Discovery of patient-specific tumor antigens usually requires in vitro-expanded autologous tumor infiltrating lymphocytes (TILs), among which tumor antigen-specific T cells are however often rare, thus limiting sensitivity. We designed in vitro culture conditions to improve the identification of rare tumor antigen-specific CD8 TILs. This innovative yet accessible pipeline allows highly-sensitive identification of tumor antigens and cognate T cell receptors (TCRs), greatly improving the selection of candidates for personalized cancer vaccines and TCR-based cellular immunotherapies.

  Study EGAS00001005513

• RNA-seq analysis of metastatic prostate cancer solid tumor biopsies

  The prevalence and features of treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) are not well characterized in the era of modern androgen receptor (AR)–targeting therapy. We sought to characterize the clinical and genomic features of t-SCNC in a multi-institutional prospective study. Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy and were followed for survival. t-SCNC is present in nearly one fifth of patients with mCRPC and is associated with shortened survival.

  Study EGAS00001006369

• Nasal MicroRNA during Bronchiolitis and Age 6y Asthma: MARC-35 Cohort

  We analyzed data from the 35th Multicenter Airway Research Collaboration (MARC-35) study to examine the relationship between nasal airway microRNAs (miRNAs) and the risk of developing childhood asthma. MARC-35 is a multicenter prospective cohort study which enrolled infants (age Structured interviews of the parents/guardians were performed by site investigators and clinical details were collected via emergency department and hospital inpatient chart reviews. Following the index hospitalization, trained study personnel conducted telephone interviews with parents/legal guardians at six-month intervals. Participants also underwent nasal swab sampling conducted by trained site personnel during the index bronchiolitis hospitalization and during an in-person follow-up examination at about age 6 years. Total RNA was extracted from nasal swab specimens using Trizol LS reagent (ThermoFisher Scientific, Waltham, MA) and the Direct-zol RNA Miniprep Kit (Zymo Research, Irvine, CA). Small RNA-seq was performed using the PerkinElmer NEXTFLEX® small RNA-seq v3 kit with Unique Dual Indexes (PerkinElmer, Waltham, MA) and sequenced on an Illumina NovaSeq6000 sequencer using an S2 50bp PE Flowcell (Illumina, San Diego, CA). Through dbGaP, limited de-identified phenotypic data (e.g., demographics) and RNA-seq FASTQ files will be made available. Among a cohort of infants hospitalized with bronchiolitis, we applied a small RNA sequencing approach and found miRNAs were associated with asthma risk factors, and highly expressed in lung tissue and immune cells (e.g., TH cells, neutrophils). They also played key roles in mechanisms relating to asthma, such as innate immunity, airway remodeling, and IgE regulation.

  Study phs003564

• RNA-seq data of HGG PDOX study

  Study EGAS00001004633