12101 results for "cancer rna-seq"

in 53.30 milliseconds.

• CLUSTER consortium RNAseq CD19 B cell dataset of UK JIA patients.

  This study examines B cell transcriptomic profiles in Juvenile Idiopathic Arthritis (JIA) patients to investigate molecular mechanisms underlying disease heterogeneity. CD19+ B cells were isolated from peripheral blood samples and subjected to RNA sequencing to characterise gene expression patterns. The dataset includes patients with documented uveitis status to enable investigation of B cell contributions to the common JIA comorbidity.

  Study EGAS50000001123

• Determining off-target effects of splice-switching antisense oligonucleotides using short read RNAseq in neuronally differentiated human induced pluripotent stem cells

  Splice-switching antisense oligonucleotides (AONs) are designed to modulate pre-mRNA splicing, thereby for instance restoring protein expression or modifying the eventual protein to restore its function or reduce its toxicity. To determine off-target effects, RNA from neuronally differentiated human induced pluripotent stem cells transfected with splice-switching AONs was sequenced.

  Study EGAS50000001222

• WES Profiles from the CheckMate-577 Clinical Trial

  The dataset contains WES profiles of 396 patients from the CheckMate-577 (CA209-577) clinical trial whose ICF allows data deposition into a public repository. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. DNA was analyzed by Whole Exome Sequencing using Swift Biosciences Accel-NGS 2S Hyb DNA Library Kit for library preparation and hybridization using Agilent SureSelect All Exon v6, followed by sequencing on the Illumina NovaSeq platform with a 100bp paired-end strategy and a target read depth of 100M per tumor sample. Fastq files are included.

  Dataset EGAD50000002395

• Defective homologous recombination in HCC

  Backgrounds and Aims: We performed an in-depth examination of pathogenic germline (PGVs) and somatic variants in DNA damage response (DDR) genes in hepatocellular carcinoma (HCC) to explore their clinical and genomic impacts. Approach and Results: We used a merged whole exome or RNA sequencing dataset derived from in-house (n=230) and TCGA (n=362) databases of multiethnic HCC samples.

  Study EGAS00001006599

• The Berlin (BLN) panel of glioblastoma cell lines: RNAseq of human gliomasphere cell lines and matched parental tumors

  We generated a panel of nine glioma stem-like cell lines under serum-free cell culture conditions from human glioblastoma samples. In addition to clinical annotation, MR imaging and histological characterization of the parental tumor, as well as xenograft studies of tumorigenecity, transcriptomic profiling of tumor/cell line pairs by RNA sequencing has been performed.

  Study EGAS00001001167

• Whole-genome and transcriptome sequencing of primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma

  Primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma (pcAECyTCL) is a rare variant of cutaneous T-cell lymphoma with an aggressive clinical course and a very poor prognosis. We subjected tumor biopsies from patients with pcAECyTCL to whole-genome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001004332

• Molecular profiling of MBD4-deficient acute myeloid leukaemia

  We describe two cases of MBD4-deficient acute myeloid leukaemia (AML). Clinical samples were used for molecular analysis, including genomic profiling (genome and exomes), methylation analysis (RRBS) and transcriptional profiling (RNA-sequencing). An analysis and methodological description has been published: “MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML” [PMID: 30049810]

  Study EGAS00001002581

• Capture Hi-C on MM

  In situ promoter capture Hi-C on multiple myeloma cell line KMS11 in experimental triplicates. Hi-C libraries were prepared as previously described (Rao et al., 2014, http://dx.doi.org/10.1016/j.cell.2014.11.021). Promoter capture was based on 32,313 biotinylated 120-mer RNA baits (Agilent). Hi-C libraries were sequenced using Illumina HiSeq 2000 technology. The files are in FASTQ format.

  Study EGAS00001002614

• Transcriptome sequencing of myelodysplasia

  Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. We also studied bone marrow CD34+ cells and bone marrow mononuclear cells obtained from three healthy adults each.

  Study EGAS00001002346

• Transcriptomic analysis of TFEB overexpression in LT-HSC, ST-HSC and MEP

  Long-term hematopoietic stem cells (LT-HSC), Short-term hematopietic stem cells (ST-HSC) and Megakaryocyte-erythrocyte progenitors (MEP) were sorted from human cord blood and cultured overnight before transduction with lentivirus to overexpress GP91 (CTRL) or TFEB. Three (LT-HSC ans ST-HSC) or six (MEP) days later, BFP+ transduced cells were sorted for RNA extraction and sequencing.

  Study EGAS00001004969