7205 results for "({!join from=dataset_studies to=id v=$q1}) OR ("transcriptome" OR "RNA-seq" OR "rna sequencing" OR "rna-sequencing")"

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• Research for biological features by gene expression analysis and biomarkers at diagnosis/therapeutics in lung cancer

  WGS, WES, ATAC-seq and methylation analysis with DNA harvested from lung cancer organoids established from surgery, biopsy, pleural effusion, sputum and blood samples of patients. RNA-seq analysis with RNA harvested from lung cancer organoids established from surgery, biopsy, pleural effusion, sputum and blood samples of patients.

  Study JGAS000609

• Research for biological features by gene expression analysis and biomarkers at diagnosis/therapeutics in lung cancer

  WGS, WES, ATAC-seq and methylation analysis with DNA harvested from lung cancer organoids established from surgery, biopsy, pleural effusion, sputum and blood samples of patients. RNA-seq analysis with RNA harvested from lung cancer organoids established from surgery, biopsy, pleural effusion, sputum and blood samples of patients.

  Study JGAS000557

• Gene expression analysis of clear cell renal cell carcinoma

  To identify genes that are differentially expressed across different conditions (cancer vs normal, normoxic vs hypoxic), we performed RNA-seq in 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions.

  Study EGAS50000001324

• An epigenomics time course analysis of covid19 patients from Quebec, Canada

  Investigating the cellular and epigenetic changes at play in severely ill hospitalized COVID-19 patients at admission and how it evolves with prognosis. Single-cell RNA-seq analysis done on longitudinal samples highlighted changes in the monocytic compartment, which we explored using whole-genome epigenomics methods (ATACseq abd WGBS).

  Study EGAS00001005468

• GENCORD2_RNAseq

  GENCORD2 RNA-seq BAM files using BWA

  Dataset EGAD00001000425

• Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (UC-GENOME): A Bladder Cancer Advocacy Network (BCAN)-Led Collaborative Research Pilot Study

  UC-GENOME is a real-world cohort of patients with metastatic urothelial carcinoma (UC). The study consisted of two co-equal aims: 1) to provide targeted DNA sequencing for clinical decision making at no cost to patients; and 2) to create a resource for collaborative translational science including a clinically annotated biobank. The submitted data represents the foundational analysis of 218 patients accrued at 7 academic medical centers. The analysis includes 176 patients with both targeted DNA sequencing and RNA sequencing. The genomic data was combined with clinical variables to model response to chemotherapy and immune checkpoint inhibitors (ICI). Due to additional sharing restrictions, data from one site can be found in phs003094.

  Study phs003066

• Inhibition of CDK4/6 Promotes CD8 T Cell Memory

  Inhibitors of Cyclin-Dependent Kinase 4 and 6 (CDK4/6) have been recently deployed for the treatment of advanced breast cancer. Despite their success, the mechanism of action of these drugs is unclear. In mice, treatment with a CDK4/6 inhibitor improve T cell memory responses and protect mice against tumor rechallenge. We aimed to identify the correlates of this finding in human subjects. In this study, blood was collected from 5 breast cancer patients before and during treatment with the CDK4/6 inhibitors abemaciclib or palbociclib. Blood was also collected from 2 breast cancer patients who did not receive a CDK4/6 inhibitor. Recently activated CD8 T cells (CD45RO+ CD45RA+) were sorted and subjected to single-cell RNA sequencing.

  Study phs002448

• Urothelial Cancer - Genomic Analysis to Improve Patient Outcomes and Research (UC-GENOME): a Bladder Cancer Advocacy Network (BCAN)-Led Collaborative Research Pilot Study - for Samples Collected at Johns Hopkins

  UC-GENOME is a real-world cohort of patients with metastatic urothelial carcinoma (UC). The study consisted of two co-equal aims: 1) to provide targeted DNA sequencing for clinical decision making at no cost to patients; and 2) to create a resource for collaborative translational science including a clinically annotated biobank. The submitted data represents the foundational analysis of 218 patients accrued at 7 academic medical centers. The analysis includes 176 patients with both targeted DNA sequencing and RNA sequencing. The genomic data was combined with clinical variables to model response to chemotherapy and immune checkpoint inhibitors (ICI).The larger dataset for this study can be found in dbGaP study phs003066.

  Study phs003094

• Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer

  Mechanisms of acquired resistance to immune checkpoint inhibitors (ICIs) are poorly understood. The purpose of this study was to investigate whether alterations in genes encoding components of the HLA Class I antigen processing and presentation machinery or interferon signaling pathways play a role in acquired resistance to PD-1 or PD-L1 antagonistic antibodies. Whole exome sequencing was performed on tumor samples collected from patients with advanced non-small cell lung cancer at the time of resistance to PD-1 axis inhibitors and on available matched pre-treatment and normal samples. Patient-derived xenografts successfully established from the ICI-resistant samples were also exome sequenced. Additionally, RNA sequencing was performed on cases with sufficient tissue.

  Study phs001464

• Single Cell Genomic Analysis of Lymphoma

  Our study aimed to define the extent of heterogeneity between anatomically separated tumor manifestations in follicular lymphoma at single-cell resolution. We subjected single-cell suspensions derived from nodal, synchronously-acquired fine needle aspirations from two distinct tumor sites to high-throughput microfluidics-based single-cell RNA sequencing. By comparing the relative composition of the tumor subpopulations between the two tumor sites, we found that some patients can exhibit site-to-site differences. While the overall composition of the tumor microenvironment did not differ significantly between sites, we did detect a specific correlation between site-to-site tumor heterogeneity and T follicular helper cell abundance. Our study demonstrates the significant limitations of a solitary biopsy in defining the full scope of a patient's disease.

  Study phs002188