14995 results for "cancer studies using rna-seq"

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• 450K_DKFZ_JMML_DBL

  DNA methylation analysis from primary human JMML and normal blood samples using 450K

  Dataset EGAD00010001296

• ADME_gene_expression

  Gene expression for 303 ADME and ADME related genes (averaged log2 signal intensities using Human-WG6v2 Expression BeadChip)

  Dataset EGAD00010001709

• Average_5mC_genome_wide

  Average genome-wide methylation levels per sample at different time points using nanopolish calls. Data from 8 individuals.

  Dataset EGAD00010002412

• Average_5hmC_genome_wide

  Average genome-wide hydroxymethylation levels per sample at different time points using megalodon calls. Data from 8 individuals.

  Dataset EGAD00010002419

• Whole-genome sequencing

  Variant calls from whole-genome sequencing of Ly1-07 using Complete Genomics paired-end sequencing service.

  Dataset EGAD00001004783

• PacBio medulloblastoma datasets

  PacBio data from 5 medulloblastoma tumor-normal pairs. The data consists of BAM files aligned using NGMLR

  Dataset EGAD00001010852

• PML complete dataset

  We generated single-cell transcriptomics, single-nuclei chromatin accessibility, CITE-seq and Multiomics of patients with PML. Pools are genetically multiplexed across donors, genotypic variation is included in this dataset to enable demultiplexing.

  Dataset EGAD50000000197

• EBNA2 ChIP-Re-ChIP in primary B-cells infected with EBV virus

  EBNA2 ChIP-Re-ChIP in primary bulk B cells 4 days post EBV-infection with B95-8. DNA binding elements of the viral master regulator EBNA2, EBNA2-CBF transcription factor complex or EBNA2-EBF1 transcription factor complex were analyzed to identify virally targeted genes.

  Dataset EGAD50000000301

• Target sequencing of 53 synovial sarcoma patients

  This dataset contains 138 .bam files sequenced with Illumina NovaSeq 6000. The files with the variant calling performed to the sequencing data, as well as the clinical data (phenotype) extracted during the sample extraction.

  Dataset EGAD50000000743

• Strand-seq data of six CK-AML patient samples and three matching PDXs

  We performed strand-specific single-cell sequencing of six primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of three matching patient-derived xenografts (PDXs). The dataset contains BAM files for each cell.

  Dataset EGAD50000000634

• Dataset of Recurrent resistance mutations to lirafugratinib delineate treatment sequences for FGFR2-driven tumors

  This dataset is made of 23 pairs of RNAseq and 36 pairs of Exome-seq, both sequenced from Illumina Novaseq. This includes 47 samples, composed of 25 tumors, 13 healthy and 9 xenograft

  Dataset EGAD50000001981

• BLUEPRINT Methylome saturation and COMET analysis of monocyte samples

  Bisulfite-Seq of CD14-positive, CD16-negative classical monocyte samples for methylome saturation and COMET analysis

  Dataset EGAD00001001261

• Chromatin accessibility in human monocytes differentiation

  This dataset consists of ATAC-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 39 samples.

  Dataset EGAD00001007953

• Bulk RNAseq with monocyte spike-ins

  This dataset contains bulk transcriptomes from the operable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19), used to verify the deconvolution method used for the scRNA-seq dataset.

  Dataset EGAD00001010306

• Tam-seq of germline samples for HGSOC copy-number signatures study

  This dataset contains targeted amplicon sequencing of Germline DNA extracted from 56 blood samples. They were sequenced on Illumina HiSeq 2500 and aligned to human genome assembly GRCh37 (hg19)to produce 127 bam files (2-3 technical replicates per sample).

  Dataset EGAD00001004172

• Genetic and epigenetic characterization of adenoid cystic carcinoma

  Whole genome sequences of ACC primagrafts, Histone modification maps and transcription factor binding maps for ACC primagrafts and primary tumors. Processed ChIP-seq data is available on GEO under accession number GSE76465.

  Dataset EGAD00001001662

• Studies in the Pathogenesis of Systemic Capillary Leak Syndrome (SCLS, Clarkson Disease)

  Systemic capillary leak syndrome (Clarkson disease) is an ultra-rare disease of unknown etiology. Patients experienced transient and recurrent episodes of hypotensive shock and massive peripheral edema due to plasma extravasation, often precipitated by minor viral infections. Disease onset occurs most frequently in middle age, and there is no family history. More than 90% of patients with the disease have monoclonal gammopathy of unknown significance (MGUS). The goal of the study is to determine pathogenic mechanisms and identify genetic underpinnings of the disease. Toward this end, we performed whole genome sequencing (WGS).

  Study phs003261

• A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk

  Identification of the genes and processes mediating genetic association signals for complex diseases represents a major challenge. As many of the genetic signals for type 2 diabetes (T2D) exert their effects through pancreatic islet-cell dysfunction, we performed a genome-wide pooled CRISPR loss-of-function screen in a human pancreatic beta cell line. We assessed the regulation of insulin content as a disease-relevant readout of beta cell function and identified 580 genes influencing this phenotype. Integration with genetic and genomic data provided experimental support for 20 candidate T2D effector transcripts including the autophagy receptor CALCOCO2. Loss of CALCOCO2 was associated with distorted mitochondria, less proinsulin-containing immature granules and accumulation of autophagosomes upon inhibition of late-stage autophagy. Carriers of T2D-associated variants at the CALCOCO2 locus further displayed altered insulin secretion. Our study highlights how cellular screens can augment existing multi-omic efforts to support mechanistic understanding and provide evidence for causal effects at genome-wide association studies loci.

  Dataset EGAD50000000518

• Transcriptomic profiles studies CAREs group - IDIBGI

  The purpose of this DAC document is to outline the principles and procedures governing access to the transcriptomic data generated from endothelial progenitor cells, or any biological origin from patients. Data Access Policy: 1) Access to this dataset is restricted and subject to approval by the DAC to ensure ethical and legal compliance. 2) The DAC reserves the right to evaluate all applications for access based on: 2.1) The scientific validity and merit of the proposed research. 2.2) The ethical considerations and adherence to data protection regulations, including GDPR. 2.3) The qualifications and affiliations of the applicants. 3) Applicants must submit a detailed research proposal, including objectives, methods, and anticipated outcomes. 4) Data usage is limited to the specified research project approved by the DAC. Any secondary use of the data requires additional approval. Confidentiality: All applicants must agree to maintain the confidentiality of the dataset. Personal identifiers have been pseudonymized to protect patient privacy. Application Process: 1) Researchers must complete the application form provided by the DAC. 2) Submit proof of ethical approval and relevant certifications for their research project. 3) Provide a signed agreement affirming adherence to the DAC's terms and conditions.

  Dac EGAC50000000607