12082 results for "cancer rna-seq"

in 20.05 milliseconds.

• BLUEPRINT September 2016, ChIP-Seq for memory B cell from venous blood, on Genome GRCh38

  ChIP-Seq data for 1 sample(s) for memory B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001002950

• BLUEPRINT September 2016, ChIP-Seq T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38

  ChIP-Seq data for 4 sample(s) T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38. 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001002952

• T-cell receptor sequencing of tumor-infiltrating lymphocytes (TIL) in breast cancer

  The spatial distribution of tumor-infiltrating lymphocytes (TIL) predicts breast cancer outcome and response to systemic therapy, highlighting the importance of an intact tissue structure for characterizing patients’ tumors. Here, we present ST-FFPE, a spatial transcriptomics method for the analysis of formalin-fixed paraffin-embedded samples, which opens the possibility of interrogating widely available archival tissue. The method involves extraction, exome capture and sequencing of RNA from different tumor compartments microdissected by laser-capture, and can be used to study the cellular composition of various tumor environments. Focusing on triple-negative breast cancer (TNBC), we characterized T cells, B cells, dendritic cells, fibroblasts and endothelial cells in both stromal and intra-epithelial compartments. We found a highly variable spatial distribution of immune cell subsets among tumors. This analysis revealed that the immune repertoires of intra-epithelial T and B cells were consistently less diverse than those of stromal T and B cells. T-cell receptor (TCR) sequencing confirmed a reduced diversity and revealed higher clonality of intra-epithelial T cells relative to the corresponding stromal T cells. Analysis of the top ten dominant clonotypes in the two compartments showed a majority of shared but also some unique clonotypes both in stromal and intra-epithelial T cells. Hyperexpanded clonotypes were more abundant among intra-epithelial than stromal T cells. These findings validate the ST-FFPE method and suggest an accumulation of antigen-specific T cells within tumor core. Because ST-FFPE is readily applicable for analysis of previously collected tissue samples, it could be useful for rapid assessment of intratumoral cellular heterogeneity in multiple disease and treatment settings.

  Study EGAS00001007125

• Whole-genome-sequencing, Whole-exome-sequencing and RNA-sequencing in Sporadic ALS

  To identify the genetic cause and modifiers of Sporadic ALS, we performed Whole-genome-sequencing, Whole-exome-sequencing and RNA-sequencing of Sporadic ALS patients.

  Study JGAS000393

• ICR_RNASeq_pHGG

  RNA sequencing of paediatric high grade gliomas and diffuse intrinsic pontine gliomas. RNA was sequenced from fresh frozen surgical material or from primary cells cultured under stem cell conditions. RNA was subjected to Illumina whole transcriptome paired end sequencing. Data is provided as paired-end FASTQ files

  Dataset EGAD00001004116

• Gene Expression and Biomarker Utility in Post-Mortem Samples

  The FAA Functional Genomics Team examined the feasibility of analyzing gene expression profiles using post-mortem brain, lung, muscle, and blood samples collected from aviation accident fatalities, with the goal of validating post-mortem extracted RNA for use in RNA sequencing. We compared the RNA sequencing results obtained from THC-positive and THC-negative samples to determine whether RNA sequencing on samples collected from aviation accident fatalities was possible and if any differences in gene expression associated with THC consumption were detectable post-mortem. The study population included 57 males of indeterminant age who perished in general aviation accidents and for whom post-mortem toxicological testing identified delta-9-THC or its primary or secondary metabolites, as well as negative controls. We determined that RNA sequencing on post-mortem aviation accident fatality samples is possible, and further identified genes showing differential expression in lung and muscle between THC-positive and THC-negative samples. We conclude that post-mortem tissue samples collected from aviation accident fatalities are suitable for gene expression profiling, but caution researchers that such samples have low RNA integrity numbers and some degree of microbial contamination is both probable and to be expected. Raw sequencing files (.fastq) from this study are available in dbGaP.

  Study phs003546

• Human embryo ATAC+RNA single cell sequencing samples DAC (Linnarsson)

  DAC for human embryo ATAC+RNA single cell sequencing samples

  Dac EGAC50000000657

• RNA-seq of DF149 cells – a patient-derived xenograft model of ascites-derived, homologous recombination repair-proficient, high-grade serous ovarian carcinoma – cultured in vitro and isolated after 8 hours treatment with DMSO control (3 x biological replicates) and 2.5 µM CBL0137 (3 x biological replicates)

  Background: High-grade serous ovarian carcinomas (HGSCs) are a heterogeneous subtype of epithelial ovarian cancers and include serous cancers arising in the fallopian tube and peritoneum. These cancers are now subdivided into homologous recombination repair (HR)-deficient and proficient subgroups as this classification impacts on management and prognosis. PARP inhibitors (PARPi) have shown significant clinical efficacy, particularly as maintenance therapy following response to platinum based chemotherapy in BRCA-mutant or homologous recombination (HR)-deficient HGSCs in both the 1st and 2nd line settings. However, PARPi have limited clinical benefit in HR-proficient HGSCs which make up almost 50% of HGSC and improving outcomes in these patients is now a high priority due to the poor prognosis with current standard of care. There are a number of potential lines of investigation including efforts in sensitizing HR-proficient tumors to PARPi. Herein, we aimed to develop a novel combination therapy by targeting SSRP1 using a small molecule inhibitor CBL0137 with PARPi in HR-proficient HGSOCs. Experimental design: We tested anti-cancer activity of CBL0137 monotherapy using a panel of HGSOC cell lines and patient-derived tumor cells in vitro. RNA sequencing was used to map global transcriptomic changes in CBL0137-treated patient-derived HR-proficient HGSOC cells. We tested efficacy of CBL0137 in combination with PARPi using HGSOC cell lines and patient-derived tumor cells in vitro and in vivo. Results: We show that SSRP1 inhibition using a small molecule, CBL0137, that traps SSRP1 onto chromatin, exerts a significant anti-growth activity in vitro against HGSC cell lines and patient-derived tumor cells, and also reduces tumor burden in vivo. CBL0137 induced DNA repair deficiency via inhibition of the HR repair pathway and sensitized SSRP1-high HR-proficient HGSC cell lines and patient-derived tumor cells/xenografts to the PARPi, Olaparib in vitro and in vivo. CBL0137 also enhanced the efficacy of DNA damaging platinum-based chemotherapy in HGSC patient-derived xenografts. Conclusion: Our findings strongly suggest that combination of CBL0137 and PARP inhibition represents a novel therapeutic strategy for HR-proficient HGSCs that express high levels of SSRP1 and should be investigated in the clinic.

  Study EGAS00001006662

• RNA sequencing of a glioblastoma PDX cohort

  Patient-derived xenograft (PDX) models represent an essential tool for the preclinical evaluation of novel targeted therapies and their combinations. In this project, we molecularly characterized a comprehensive panel of glioma PDX models with well conserved molecular and pathological features over multiple passages. PDX samples were subjected to next generation sequencing (NGS). Characterization of cancer-relevant features including driver mutations or cellular processes was performed using mutational and gene expression data in order to identify potential biomarker or treatment targets in glioblastoma. In summary, we reported a newly established and molecularly characterized panel of glioma PDX models with high relevance for translational preclinical research.

  Study EGAS00001007119

• 41 fibroblast RNAseq samples of pediatric patients with childhood epilepsy and developmental delay

  We used RNA sequencing of patient fibroblasts to find a genetic diagnosis in patients with exome-negative childhood epilepsy. RNA extracted from 41 individuals' cultured fibroblasts (passage 3-6) was collected and sequenced at a depth of 90-110 paired reads per sample.

  Study EGAS50000000792