14980 results for "cancer studies using rna-seq"

in 19.30 milliseconds.

• The data access committee for "Validation of cfDNA fragmentome analyses for early detection of liver cancer"

  Dac EGAC00001003543

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

  Study EGAS00001004655

• A renal cell carcinoma tumorgraft platform to advance precision medicine

  Study EGAS00001005516

• Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia (HIPO, H005)

  Study EGAS00001006361

• Angiosarcoma_whole_exome

  Extension of angiosarcoma whole genome sequencing study

  Study EGAS00001000588

• Angiosarcoma_RNA_sequencing

  Extension of angiosarcoma whole genome sequencing study

  Study EGAS00001000590

• FFPE_whole_genome_pilot

  To assess feasibility of whole genome sequencing

  Study EGAS00001001967

• Angiosarcoma_targeted_pulldown_cancer_gene_panel

  Extension of angiosarcoma whole genome sequencing study

  Study EGAS00001000589

• Deep_sequencing_of_melanoma_for_driver_mutations

  Deep sequencing of melanoma for driver mutations

  Study EGAS00001000857

• Angiosarcoma targeted pulldown cancer gene panel

  Extension of angiosarcoma whole genome sequencing study

  Dataset EGAD00001001064

• NECC WXS

  Whole exome sequencing of neuroendocrine cervical cancer

  Dataset EGAD00001006391

• NINDS Deep Sequencing for the Detection of Viral Sequences in Primary Progressive Multiple Sclerosis Brains

  Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples (n = 7) from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed, and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue (Chan et al., 2014). Data from the primary progressive multiple sclerosis (PPMS) brain specimens (n = 14) and Normal Control brain specimens (n = 14) are also submitted here. All the subjects studied here (encephalitis, PPMS, and controls) were selected from existing collections at the Rocky Mountain and UCLA brain banks. These selections were performed by the directors at the two centers (Dr. Corboy at RM and Nagra at UCLA) based on clinic information provided at the time of collection. All the specimens are from deidentified deceased individuals. The submitting investigators have no identifying information on any of these subjects. To avoid confusion, the dbGaP Subject IDs are identical to the brain bank identifying numbers.

  Study phs000715

• 18 Whole Exome Sequencing for Radiation Induced-Meningiomas

  Purpose: Majority of pediatric cancers require the irradiation of the central nervous system (CNS), and as more patients survive into adulthood from improved oncological therapy the sequelae of brain radiation are increasing in prevalence. Radiation-induced meningiomas (RIMs), one such secondary effect, demonstrate a clinically more aggressive behaviour than sporadic meningiomas (SMs). We aimed to describe the genomic mutational landscape of RIMs.Methods: We analyzed a principal cohort of 18 RIMs, with 31 RIMs overall, from patients who received childhood radiation therapy and 30 SMs, as a comparator population. We performed a multiplatform integrative genomic analysis; including methylation, whole exome and RNA sequencing. Results: RIMs exhibited a five-fold increase in copy number alterations, commonly the loss of chromosome 1p (17/18 RIMs) and 22q (17/18 RIMs), which was significantly more than observed in sporadic meningiomas. Furthermore, RNA sequencing data revealed an NF2 gene fusion event in 35.3% of RIMs. In all 6 cases, there was a complete NF2 exon spliced into a complete exon of a reciprocal gene, suggesting that the breakpoints of genomic rearrangement are intronic. All tumours with the NF2 fusion also possessed monosomy of chromosome 22q, rendering the cells with homozygous disruption of NF2. Clinically, RIMs with the NF2 fusion exhibited ill-defined borders and a tendency to develop in anatomic frontal location. Also, targeted sequencing panel confirmed that RIMs had fewer nonsynonymous NF2 mutations (6.5% vs. 30% in SM) and absence of mutations in TRAF7, SMO, KLF4, PIK3CA and AKT1, genes traditionally involved in SMs.Conclusion: Our study demonstrates that RIMs have distinct genomic drivers of oncogenesis as compared to SMs, specifically NF2 inactivation through fusion event. Radiation therapy possibly triggers genomic structural rearrangements through error-prone repair of double-stranded DNA breaks.

  Study EGAS00001002317

• Whole transcriptome sequencing data of 3 histiocytic tumors with CLTC::SYK fusions

  The 3 tumor samples are PMLBM000JFR, PMLBM000JFT, and PMLBM000JFF. All samples are from different patients: Case 9 (PMLBM000JFR), Case 10 (PMLBM000JFT), and Case 12 (PMLBM000JFF) from the article by Kemps et al (Blood 2024 - In production). Methods: Total RNA was isolated and the generated libraries were sequenced on a NovaSeq 6000 (as described in Hehir-Kwa, et al. JCO Precis Oncol 2022). Data files: Provided are .cram and .crai files.

  Dataset EGAD50000000834

• TTV018 RORC IBD-associated genotype effects on RORgT expression and function in ex vivo T cells (2019-02-15)

  RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment. 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/ . This dataset contains all the data available for this study on 2019-02-15.

  Dataset EGAD00001004777

• Cell types of the human retina and its organoids at single-cell resolution. Cowan et al

  Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers, and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas.

  Dataset EGAD00001006350

• RNA sequencing of multiple myeloma identifies genes dysregulated by structural variants.

  Multiple myeloma is a disease of structural changes brought about by copy number abnormalities and translocations. Many of these changes result in super-enhancers being placed next to key oncogenes. Here, we have investigated which genes are commonly dysregulated by these changes.

  Study EGAS00001003411

• LSC RNA-Sequencing

  To infer the proteomic Mito signature in the LSC subcompartiment, myeloid blasts for 10 patients from the discovery cohort were FACS-sorted into CD34-GPR56+NKG2DLigands- (CD34-), alias 61dc5fb798e2520001702c03 CD34+GPR56+NKG2DLigands- (CD34+), alias 61dc5fb798e2520001702c03 Detailed gating strategy will be described in Donato, Correia, Andresen and Trumpp et al., (manuscript in preparation)

  Dataset EGAD00001008488

• Single cell sequencing on whole bone marrow of NBM and AML

  To generate a cellular taxonomy of the human NBM and AML, representing both rare hematopoietic stem/progenitor cells (HSPCs) and stromal niche populations, allowing assessment of their cellular diversity and predicted intercellular signaling, we performed single cell RNA sequencing (scRNAseq) on viably frozen bone marrow (BM) aspirates from four healthy donors and 6 NPM1+ AML patients at diagnosis

  Dataset EGAD00001011057