14978 results for "cancer studies using rna-seq"

in 16.37 milliseconds.

• Single cell RNA-sequencing of glioblastoma stem cell lines

  Single cell RNA-sequencing of glioblastoma stem cell (GSC) lines with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome using CellRanger.

  Dataset EGAD00001006804

• Osteosarcoma capture-based RNA sequencing

  This dataset includes 23 specimens from osteosarcoma patients (primary, relapsed, metastatic). It contains bam files from RNA sequencing using a library in which coding regions of cDNA are captured and short-read, paired-end sequencing.

  Dataset EGAD00001008434

• Paired RNA sequencing of 30 samples RRMM (multiple myeloma)

  Paired RNA sequencing of 30 samples RRMM using Illumina TruSeq stranded mRNA kit and either HiSeq2000 or HiSeq X Ten for sequencing.

  Dataset EGAD00001009680

• Identification of Long Non-coding RNA Biomarker of Human Lupus Nephritis Disease Activity - Dataset

  Total RNA paired-end sequencing was performed on whole blood samples from 74 Lupus nephritis (LN) patients and 20 healthy controls using Illumina NovaSeq 6000.

  Dataset EGAD00001010932

• Dataset for colorectal_cancer-EXON

  Rare cancer sequencing data of 119 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008871

• Dataset for breast_cancer-EXON

  Rare cancer sequencing data of 94 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008868

• Dataset for gynecologic_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 38 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008878

• Targeted DNA sequencing of 44 urothelial cancer samples from 34 Lynch syndrome patients

  Targeted Illumina sequencing of 41 tumor tissue samples and 3 urine tumor DNA samples from 34 patients with Lynch syndrome associated urothelial cancer. Target capture was performed using the UroScout hybridization capture panel targeting the coding regions of 25 urothelial cancer genes. Sequencing libraries were constructed using the Twist Biosciences Enzymatic Fragmentation DNA Library Prep kit. Sequencing was performed using an Illumina NovaSeq 6000 instrument with 2x150 bp paired sequencing.

  Dataset EGAD50000001220

• Single cell RNA sequencing of tumor and ascites in high grade ovarian cancer

  Fastq files for single cell RNA sequencing of cells from ovarian cancer tumor and ascites (10X chromium 5' v1.1 libraries). Multiple cases are pooled in each sequencing library.

  Dataset EGAD00001006627

• CD4 T Cell Subsets in Human Metastatic Melanoma

  We used single-cell RNA-sequencing (scRNA-seq) to define CD4+ T-cell subsets in melanoma tumors from patients undergoing tumor resection. All patients received immune checkpoint blockade prior to surgery. We identified multiple subsets in the tumor with transcriptional features of suppressive function, including TR1 cells and FOXP3+ Treg cells. Based on transcriptional profiles, classical helper T cell subsets were not prevalent.

  Study phs003816

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  arious peripheral blood immune cell subsets from 5 rheumatoid (RA) donors were collected ("CD16p_Mono", "CL_Mono???, "DN_B", "Fr_II_eTreg???, "mDC???, "Mem_CD4" , "Naive_B" , "Naive_CD4" , ???Neu", "NK" , "pDC" , "Plasmablast", ???SM_B", "Tfh", "Th1", "Th17", "Th2" , "USM_B"). The patients were analyzed again longitudinally after abatacept treatment. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.

  Study JGAS000602

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  Various peripheral blood immune cell subsets from 39 healthy volunteers and 50 rheumatoid (RA) donors were collected ("CD16p_Mono", "CL_Mono???, "DN_B", "Fr_II_eTreg???, "mDC???, "Mem_CD4" , "Naive_B" , "Naive_CD4" , ???Neu", "NK" , "pDC" , "Plasmablast", ???SM_B", "Tfh", "Th1", "Th17", "Th2" , "USM_B"). 15 RA patients were analyzed longitudinally. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered.

  Study JGAS000598

• The genomic landscape of Burkitt Lymphoma

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing and RNA sequencing of Burkitt Lymphomas . Burkitt lymphomas are the most common B-cell lymphomas in childhood. Analyses were performed in concordance with the guidelines of the ICGC. The results define the genomic landscape of structural variants, somatic single nucleotide variants and mutational signatures in these lymphomas.

  Study EGAS00001002198

• Molecular landscape of blastic plasmacytoid dendritic cell neoplasm

  Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive malignancy assumed to originate from plasmacytoid dendritic cells (pDCs), which mostly affects the skin, bone marrow and lymph nodes and sequentially other organ systems. We applied paired WES/RNA-seq combined with genome-wide copy-number analysis to characterize 47 BPDCN patients regarding mutational drivers, cytogenetic aberrations and gene-expression profiles.

  Study EGAS00001006166

• Extensive patient-to-patient single nuclei transcriptome heterogeneity in pheochromocytomas and paragangliomas

  Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors of varied genetic makeup, associated with high cardiovascular morbidity and a variable risk of malignancy. We focused on PCPG tumors with germline SDHB and RET mutations, representing distinct prognostic groups with worse or better prognoses, respectively. We applied single-nuclei RNA sequencing (snRNA-seq) on tissue samples from 11 patients.

  Study EGAS00001006230

• Genetic regulation of gene expression in human brain cell types

  We leveraged single nuclei RNA-seq from 192 human brain samples to map cis-eQTLs in 8 brain cell types. We found extensive cell-type specific genetic effect on gene expression and integrated our results with GWAS to identify putative novel risk genes for brain disorders and the cell types in which the disease mechanisms are likely active.

  Study EGAS00001006345

• A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours

  We generated a single-cell RNA-seq atlas capturing over 100,000 cells spanning all stages of the mouse cerebral development. By examining data from over 100 cerebral tumour samples, our study reveals that, despite the phenotypic/genotypic differences between the tumour types, they are all comprised of developmental sublineages that map most closely to embryonic or juvenile stages of development.

  Study EGAS00001006237

• Tumor HTG EdgeSeq from metastatic castrate resistant prostate cancer

  This dataset contains tumor bulk HTG EdgeSeq from patients with metastatic castrate resistant prostate cancer. RNA libraries were prepared following manufacturer's user guide (HTG Molecular Diagnostics). Each library was sequenced in HTG EdgeSeq system.

  Study EGAS00001004852

• Integrated Metabolic Profiling and Gene Expression Analysis Reveals Therapeutic Modalities in Breast Cancer

  In this study, we performed metabolite profiling and RNA-sequencing on human breast cancer tumors and normal breast tissue samples, including triple negative breast cancer (TNBC), estrogen receptor positive breast cancer (ER+) and paired normal samples, and patient-derived xenografts (PDX) samples. Here, we report two distinctive groups defined by metabolites; a TNBC-HIGH group that shows high levels of pyrimidine pathway metabolites and biosynthetic enzymes, and an ER-HIGH group that shows high levels of fatty acid and arginine biosynthesis intermediates. We identify different metabolic enrichment profiles between cell lines grown in vitro vs. in vivo; cell lines grown in vivo recapitulate patient tumors metabolic profiles. Further, we identify a subset of genes that strongly correlates with the TNBC-HIGH metabolic profile using integrated metabolic and gene expression profiling, which strongly predicts patient prognosis when tested on larger human datasets. As a proof-of-principle, when we target TNBC-HIGH metabolic dysregulation with a pyrimidine biosynthesis inhibitor (Brequinar), and/or a glutaminase inhibitor (CB-839), we observe therapeutic efficacy and decreased tumor growth in representative TNBC cell lines, murine p53-null mammary tumors, and in vivo patient-derived xenografts (PDXs) upon multi-agent drug treatment. This study highlights potential new therapeutic opportunities in breast cancers guided by a genomic biomarker, which could prove impactful for breast cancers that rapidly proliferate.

  Study phs002396

• Treg cell subset-specific gene expression patterns in human head and neck cancer

  Backgrand: The occurrence of head and neck cancer has been increased all over the world. Although the prognosis has been improved by using several treatment modalities including immunotherapy, it is still unsatisfying. It is still unclear why the immunotherapy is effective only for partial amount of patients. To resolve this problem and to make a new treatment strategy based on human immune system, further investigation of antitumor immunity is required. Regulatory T (Treg) cells play critical roles in human immune responses including antitumor immunity. Therefore, the research to elucidate Treg function is strongly urged to clarify the mechanisms of antitumor immunity. Methods: We performed RNA-seuencing analysis of regulatory T cells infiltrating head and neck cancer. We devided into four populations, DP, CD25+, CTLA4+, DN and analyzed gene expressions. Results: The gene expression patterns of Treg-related genes were different between CD25+ cells and CD25- cells. Furthermore, DP cells had unique gene expression pattern compared to other populations. Conclusions: We found Treg cells infiltrating head and neck cancer had high expression levels of Treg-related genes and DP cells had unique gene expression pattern that may become a target of new treatment strategy. Regulatory T (Treg) cells play critical roles in human immune responses including antitumor immunity. Therefore, the research to elucidate Treg function is strongly urged to clarify the mechanisms of antitumor immunity.

  Study JGAS000135

• Circulating Tumor Cell Heterogeneity in Neuroendocrine Prostate Cancer by Single Cell Copy Number Analysis

  Neuroendocrine prostate cancer (NEPC) is an aggressive variant of prostate cancer that may arise de novo or develop from pre-existing prostate adenocarcinoma as a mechanism of treatment resistance. Combined loss of tumor suppressors RB1, TP53, PTEN are frequent in NEPC but also present in a subset of prostate adenocarcinomas. Most clinical and preclinical studies support a trans-differentiation process, whereby NEPC arises clonally from a prostate adenocarcinoma precursor during the course of treatment resistance. Here we highlight a case of NEPC with significant intra-patient heterogeneity observed across metastases. We further demonstrate how single-cell genomic analysis of circulating tumor cells combined with phenotypic evaluation of cellular diversity can be considered as a window into tumor heterogeneity in patients with advanced prostate cancer. We performed whole genome sequencing of circulating tumor cells (CTCs) from patients with castration resistant adenocarcinoma (n=4) and neuroendocrine prostate cancer (n=8). CTCs were collected via Epic Sciences platform and single CTC genomic data (n=215) generated via Illumina NextSeq500. 

  Study phs002462

• Research for drug discovery and elucidation of pathophysiology using disease-specific iPS cells

  We investigated roles of KRAS on stemness maintenance and differentiation propensity in the context of induced pluripotent stem cells (iPSCs) using isogenic KRAS mutant (G13C/WT) and wild-type (WT/WT) iPSCs from the same RAS-associated autoimmune lymphoproliferative syndrome-like disease (RALD) patients. Exome-seq analysis was conducted to compare gene profiles of WT/WT and G13C/WT iPS cells. We have not found any differences of gene mutation in the two genotypes.

  Study JGAS000136

• Chromatin run-on and RNA sequencing of fibrolamellar carcinoma

  Fibrolamellar carcinoma (FLC) is a rare, therapeutically intractable liver cancer that disproportionately affects youth. Here we used chromatin run-on sequencing to characterize the enhancer landscape in FLC and RNA sequencing to identify dysregulated genes in FLC.

  Study EGAS00001004169

• Meta-Analysis of Genome-Wide Association Studies of Bladder Cancer Risk

  This meta-analysis consists of genome-wide genotype for 13,447 cases and 342,580 controls of European ancestry to identify novel susceptibility loci for bladder cancer. Cases were defined as histologically confirmed primary carcinoma of the urinary bladder of all stages, including carcinoma in situ (International Classification of Diseases for Oncology, C670-C679, 188). All histologic subtypes were included. Summary-level results for the association between genotyped/imputed variants and risk of bladder cancer are included.

  Study phs003342

• Citrate synthase novel variant rewires TCA cycle to promote colorectal cancer progression

  H3K4me3, IgG, and Input ChIP-seq in overexpression of pLV Control, CS-FL and CS-ΔEx4 in SW1116 cells

  Dataset EGAD00001015543