986e3270-53f6-45e1-8d37-74dd7fca6cd7 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006852 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:NABUCCO cohort 1 sequencing data. The dataset includes:
* Whole exome DNAseq pre-treatment on tumor samples (n=24) matched with blood samples (n=24)
* RNAseq pre-treatment on tumor samples (n=18)
* RNAseq post-treatment on tumor samples (n=18). Not all pre-treatment samples are linked with pre-treatment samples
* High coverage Whole exome DNAseq on pre-treatment tumor samples (n=3) matched with post-treatment metastasized lymph nodes isolated with laser microdissection (n=3)
* All samples are labelled with the response phenotype (Complete Responder or Non-Complete Responder)
| EGAD00001006250 | EGA
Project description:Data from NABUCCO cohort 2 (NCT03387761). This dataset includes Whole exome DNA sequencing
on bladder tumor samples matched with blood samples for patients from NABUCCO Cohort 2 (Cohort 2A and Cohort 2B). The data is pre-treatment
| EGAD00001009864 | EGA
Project description:Data from NABUCCO cohort 1 (NCT03387761). This dataset includes Whole exome DNA sequencing
on bladder tumor samples (n=24) matched with blood samples (n=24). The data is pre-treatment.
| EGAD00001006850 | EGA
Project description:In this study we characterized genomic alterations in three bladder cancer patients with metastatic disease courses. Multiple regions were procured by laser microdissection or punctures from primary tumor, lymph node metastases and from distant metastases. Data provided here consist of 35 Bam files for WES (32 Tumors and 2 blood, 1 adjacent normal)
| EGAD00001002772 | EGA
Project description:We have induced experimental autoimmune encephalomyelitis (EAE) in mice to mimic B cell aggregate formation as seen in progressive multiple sclerosis patients. Aggregates and regular central nervous system infiltrates were dissected using laser capture microdissection. RNA was collected using commercially available kits and subjected to RNA sequencing. Samples were compared to draining lymph nodes and to another EAE model, which had no involvement of B cells.
2019-06-10 | GSE125144 | GEO
Project description:NABUCCO cohort 1 sequencing data. The dataset includes RNA sequencing pre-treatment on tumor samples (n=18) and RNA sequencing post-treatment on bladder tumor samples (n=18).
| EGAD00001006855 | EGA
Project description:Purpose: to explore the epigenomic landscape of innate immune cells stimulated with a novel adjuvant, 3M052 Methods: Mice were injected with 3M052. Draining lymph nodes were negatively selected for CD19+ and CD3+, then flow sorted into four populations: Dendritic cells (DCs), Double positive cells (DP, CD11b+BST1+), Ly6c+ cells (Ly6c), and plasmacytoid dendritic cells (pDCs). Lymph nodes were harvested at baseline (D0), 24 hours post-treatment (D1) or 28 days post-treatment (D28).
2021-12-05 | GSE180752 | GEO
Project description:Purpose: To understand the innate immune response to an adjuvant, 3M052, and yellow fever vaccine, YFV Methods: Draining lymph nodes were negatively selected for CD19+ and CD3+, then flow sorted into four populations: Dendritic cells (DCs), Double positive cells (DP, CD11b+BST1+), Ly6c+ cells (Ly6c), and plasmacytoid dendritic cells (pDCs). Lymph nodes were harvested at baseline (D0), 24 hours post-treatment (D1) or 28 days post-treatment (D28). Results: TBD Conclusions: TBD
2021-12-05 | GSE180384 | GEO
Project description:<p>Mycosis fungoides (MF) is a common extranodal T-cell lymphoma primarily arising in the skin. In early disease stages, MF presents as skin patches and plaques that in some cases may progress to tumor and disperse to lymph nodes and other internal organs. The 10-year overall survival is 50% in advanced stages. Early diagnosis is difficult as the histology overlaps with features of inflammatory skin diseases. Even when the diagnosis is established, there are no prognostic markers that predict whether the disease will be aggressive or indolent. Lastly, there are no curative treatments and MF will invariably relapse, even after aggressive chemotherapy. The disease is a diagnostic, prognostic and therapeutic challenge. The main objective of this study is to address the question of tumor heterogeneity in MF. To date, MF is considered to be monoclonal, derived from a transformed, mature memory T-cell. However, clinical observations and preliminary data suggest that MF comprises multiple subclones, which may be of importance for understanding disease evolution and resistance to therapy. We plan to address this objective using Whole Exome Sequencing (WES) of MF tissue prepared by laser microdissection (LMD).</p>
| phs001877 | dbGaP
Project description:Hepatitis C virus (HCV) infection can result in viral chronicity or clearance. Although host genetics and particularly genetic variation in the interferon lambda (IFNL) locus are associated with spontaneous HCV clearance and treatment success, the mechanisms guiding these clinical outcomes remain unknown. Using a laser capture microdissection-driven unbiased systems virology approach, we isolated and transcriptionally profiled HCV-infected and adjacent primary human hepatocytes (PHH) approaching single cell resolution. An innate antiviral immune signature dominated the transcriptional response, but differed in magnitude and diversity between HCV-infected and adjacent cells. Molecular signatures associated with more effective antiviral control were determined by comparing donors with high and low infection frequencies. Cells from donors with clinically unfavorable IFNL genotypes were infected at a greater frequency and exhibited dampened antiviral and cell death responses. These data suggest that early virus-host interactions, particularly host genetics and induction of innate immunity, critically determine the outcome of HCV infection. Cell populations of primary human hepatocytes were collected via laser capture microdissection, their transcriptomes were amplified and analyzed via whole Illumina genome microarray. Three populations were collected: virus infected cells, cells adjacent to infected cells (“adjacent”) and mock infected cells. Cells from multiple donors were employed to address host genetic variability on our observed phenotypes. Nine different donors were assessed on 1-day post infection and three donors were assessed 3 days post infection and and four donors were assessed on 7 days post infection. For each cell population (virus infected, adjacent or mock), four biological replicate arrays were performed. In total, we analyzed 186 microarrays
2014-02-12 | E-GEOD-54648 | biostudies-arrayexpress