15120 results for "cancer studies using rna-seq"

in 18.74 milliseconds.

• HLF COPD Transcriptomics

  We generated transcriptomes of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. RNA sequencing analysis demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization.

  Study EGAS00001006602

• Transcriptomic analysis of MYC overexpression in LT-HSC.

  Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors (empty E CTRL or MYC). Six days after transduction, BFP+ transduced cells were sorted for RNA extraction and sequencing

  Study EGAS00001004970

• RNA-sequencing data from human FSHD and control skeletal muscle biopsies

  This project includes RNA-sequencing data from human FSHD and control skeletal muscle biopsies. This project includes data from 28 FSHD patients (total 37 samples, including vastus lateralis and tibialis anterior muscles) and 12 control individuals (total 24 samples, including vastus lateralis and tibialis anterior muscles).

  Dataset EGAD00001008337

• Human Biofluid RNA Atlas

  This dataset contains small RNA sequencing data and mRNA capture sequencing data from 20 different human biofluids (amniotic fluid, aqueous humor, ascites, bile, bronchial lavage fluid, breast milk, cerebrospinal fluid, colostrum, gastric fluid, pancreatic cyst fluid, plasma, saliva, seminal fluid, serum, sputum, stool, synovial fluid, sweat, tear fluid and urine). In total, 180 samples were sequenced. Files are provided in fastQ format. Samples were sequenced on a NextSeq 500.

  Dataset EGAD00001005439

• RNA-sequencing of six Pilocytic astrocytoma tumors

  Total stranded TruSeq RNA sequencing by Illumina of six tumor samples from six cases of pediatric Pilocytic astrocytoma. The data is published in the following paper: Tomic TT, Olausson J, Wilzen A, Sabel M, Truve K, Sjogren H, Dosa S, Tisell M, Lannering B, Enlund F, Martinsson T, Aman P, Abel F. A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS One. 2017 Apr 27;12(4):e0175638.

  Dataset EGAD00001003143

• Exome and RNA-sequencing data from a relapsed t(1;19) acute lymphoblastic leukemia

  Sequence data is from 4 samples from an adult patient with TCF3-PBX1 t(1;19)-positive acute lymphoblastic leukemia. Exome sequencing was performed on a skin biopsy (normal tissue control) and leukemic bone marrow biopsies taken at diagnosis and at two relapse time points. RNA-sequence data is from leukemic bone marrow from two relapse biopsies.

  Dataset EGAD00001002203

• RNA sequencing of cytokine-induced T cell responses

  Cytokines affect T cell responses by polarising them to different phenotypes. We isolated T cells from healthy platelet donors and cultured them in resting and stimulated conditions, as well as in the presence of Th1, Th2, Th17 and iTreg cocktail. In addition, T cells were stimulated in the presence of IL-10, IL-21, IL-27, IFNb and TNFa. We performed bulk RNA sequencing to assess impact of different disease-relevant cytokines upon T cell response.

  Dataset EGAD00001005291

• RNA-sequencing and targeted DNA-sequecing of human thyroid tumors and normal samples

  RNA-sequencing data: 5 normal thyroid tissues, 14 papillary thyroid carcinomas, 2 lymph node metastases, 19 poorly differentiated thyroid carcinomas and 17 anaplastic thyroid carcinomas; Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors” panel (BRIGHTCore, Brussels, Belgium): 2 normal thyroid tissues, 2 poorly differentiated thyroid carcinomas and 7 anaplastic thyroid carcinomas; 2 FASTQ files for each sample (paired).

  Dataset EGAD00001011678

• Improved Sezary cell detection and novel insights into immunophenotypic and molecular heterogeneity in Sézary syndrome

  We performed a prospective investigation in Sézary syndrome by the application of a standardized multiparameter flow cytometry, FACS-cell sorting, and RNA-sequencing for an in-depth immunophenotypic and transcriptional profiling of Sézary cells.

  Study EGAS00001005229

• TREM2+ Cells in Human Basal Cell Carcinomas

  To explore the tumor immune microenvironment heterogeneity in sporadic human basal cell carcinoma tumors, we profiled two individual patient tumors by scRNA-Seq. We identified a population of TREM2+ macrophages, which have been implicated in promoting an immunosuppressive tumor microenvironment. We identify that TREM2+ can promote tumor epithelial proliferation in an immunosuppressive independent manner.

  Study phs003242

• Dissecting Autoimmune Cellular and Molecular Networks in Vitiligo

  This study consists of suction blister biopsies of primary human skin samples, collected from healthy patients, or patients with vitiligo. Healthy patients had healthy skin sampled. Vitiligo patients had both unaffected (non-lesional) and affected (lesional) skin sampled. The generated data consists of scRNA-seq samples generated following the inDrops method (Klein et al., 2015; PMID: 26000487).

  Study phs002455

• HCC cfMeDIP-seq

  This dataset comprises 406 raw fastq files derived from 203 plasma cfDNA samples from 90 patients diagnosed with hepatocellular carcinoma (HCC). The samples include 90 baseline HCC (b-HCC) samples, collected during liver transplant or resection surgeries, and 113 postoperative follow-up (f-HCC) samples. For each sample, 10ng of cfDNA was used for library preparation utilizing cfMeDIP-seq technology based on the 5mC antibody-immunoprecipitation strategy. Libraries were validated via Bioanalyzer trace analysis and sequenced on Illumina NovaSeq 6000 or HiSeq 2500 platform with paired-end 150-bp (NovaSeq) or 125-bp (HiSeq) model for ~100 million reads per sample.

  Dataset EGAD50000000651

• SUM-seq data for spontaneous differentiation of iPSCs upon perturbation of GATA2, NR4A2 or SOX17

  We combined SUM-seq with arrayed CRISPR screening, modulating the expression of key lineage transcription factors (TFs) (GATA2 - mesoderm, SOX17 - endoderm, and NR4A2 - neuroectoderm) in hiPSCs via CRISPR interference (CRISPRi) or activation (CRISPRa) over a time course of spontaneous differentiation (days cultured in vitro: 0, 4, 12, and 18). This totalled to 54 samples (4 day/time points x 3 target TFs x 2-3 gRNAs per target x CRISPRi/a). Single-cell chromatin accessibility and gene expression data is provided as demultiplexed fastq files.

  Dataset EGAD50000001205

• SUM-seq data for Macrophage polarisation to M1 and M2 phenotypes experiment

  We stimulated iPSC-derived M0 macrophages with LPS and IFN-γ to induce M1 polarization or IL-4 to induce M2 polarization. To discern early and sustained responses at chromatin accessibility and gene expression levels, we collected samples at five time points along the two polarization trajectories; prior to stimulation (M0) and at 1-hour, 6-hour, 10-hour, and 24-hour intervals, each sampled in duplicates totaling 18 samples, and subjected them to SUM-seq library preparation. Sequenced files for both data modalities are provided as demultiplexed fastq files.

  Dataset EGAD50000001206

• Single Cell Multiome ATAC + Gene Expression sequencing

  The SHH medulloblastoma tumor 7316-178 was received through the Childhood Brain Tumor Network (CBTN). From the patient tumor, disassociated cryopreserved cells stored in 10% DMSO/FBS were used. At least 50 mg of tissue (1 M cells) was used for both samples. Disassociated cells were prepared for Single Cell Multiome ATAC + Gene Expression sequencing (10× Genomics) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq S4 200 to a depth of at least 250 M reads for snATAC-seq and 200 M reads for snRNA-seq.

  Dataset EGAD50000001515

• Identification of cell type differences in FOXN1 mutation carriers by scRNA-seq

  scRNA-seq was performed on the BD Rhapsody platform. CD45+ lymphocytes from two FOXN1het patients and one cord blood sample as control were sorted from frozen cryopreserved samples. The samples were split and each sample was stained with 4 Sampletag antibodies before Abseq staining with the BD Immune Discovery panel and 6 additional antibodies was performed to better classify immune cell subsets. The sorted and stained populations were pooled before loading onto the BD Rhapsody cartridge. The manufacturer's protocol was followed for library construction and samples were sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD50000001708

• Single cell RNA-sequencing of tissues from NSCLC patients treated with chemoimmunotherapy

  Study EGAS00001006728

• Exploration of neuroblastoma xenograft models for tumor extracellular RNA profiling in murine blood plasma

  Study EGAS00001007295

• Angiosarcoma RNA sequencing

  Extension of angiosarcoma whole genome sequencing study

  Dataset EGAD00001000738

• Validation of Gene Array to Predict Bacterial Co-infection In Adults Hospitalized with Viral Lower Respiratory Tract Infections (LRTI)

  Accurate tests for microbiologic diagnosis of lower respiratory tract infections (LRTI) are needed. Gene expression profiling of whole blood represents a powerful new approach for analysis of the host response during respiratory infection that can be used to supplement pathogen detection testing. Using qPCR, we prospectively validated the differential expression of 10 genes previously shown to discriminate bacterial and non-bacterial LRTI confirming the utility of this approach. In addition, a novel approach using RNAseq analysis identified 141 genes differentially expressed in LRTI subjects with bacterial infection. Using "pathway-informed" dimension reduction, we identified a novel 11 gene set (selected from lymphocyte, α-linoleic acid metabolism, and IGF regulation pathways) and demonstrated a predictive accuracy for bacterial LRTI (nested CV-AUC=0.87). RNAseq represents a new and an unbiased tool to evaluate host gene expression for the diagnosis of LRTI.

  Study phs001248

• NIDDK International IBD Genetics Consortium Repository Global Screening Array

  The purpose of this GWAS meta-analysis is to assess IBD risk alleles using data collected by members of the International IBD Genetics Consortium and their collaborators around the world. Data from over 30 cohorts have been identified and are being combined for analysis. Genotyping has been conducted using a variety of chips with most samples genotyped using GSAMD-24v1-0 or GSA-CHO-Custom. Individual level genotype data will be made available whenever possible (some groups are only able to provide summary statistics due to institutional and/or governmental restrictions on data sharing), together with information on sex, self-reported ancestry, IBD affection status and diagnosis. This first batch includes data from North American sites who are members of the NIDDK-funded IBD Genetics Consortium. Additional data will be provided in an update as soon as they have gone through the QC process.

  Study phs002336

• POPCOL: population-based colonoscopy.

  PopCol is a cohort study in Stockholm, Sweden that includes a data-rich set of individuals with data available from bowel symptoms questionnaires, gastroenterology visits and biospecimens (genotype and 16S sequencing from blood and stool samples, respectively). Genotyping was carried out using the Illumina HumanOmniExpressExome-8v1 arrays at the SciLifeLab NGI facility in Uppsala, Sweden. Fecal DNA was extracted from samples kept at -80°C using Qiagen 5 QIAamp DNA Stool Mini Kits and analyzed using 16S rRNA gene amplicon sequencing (in the V1-V2 hypervariable region). This was performed on the Illumina MiSeq platform at the Institute of Clinical Molecular Biology (IKMB) in Kiel, Germany. Of these, six PopCol participants were PPI users and 12 used antibiotics. The study was approved by the local Committee of Research Ethics (Forskningskommitté Syd) at Karolinska Institutet, Stockholm, in November 2001. Written informed consent was obtained from all participants

  Study EGAS00001004869

• Breast Cancer - Very young women

  This project will focus on sequencing of breast cancer from young age cancer patients characterized by age at diagnosis under 35. Based on the incidence rate by Korean National Cancer Incidence Database, breast cancer is the most common solid tumors among young adults aged 15-34 excepting thyroid cancer (Cancer statistics in Korea (2012)). This project just started from the mid of 2015. National cancer center in Korea are collecting more than 100 tumor specimens from breast cancer patients aged 20-34. Genetic features of young patients will be investigated with somatic mutation pattern, structural variations, and canonical pathways.

  Study EGAS00001001908

• An immune response network associated with blood lipid levels

  Genome-wide genotyping was performed on a population-based cohort from the capital region of Finland using the Illumina 610-Quad SNP microarray

  Study EGAS00000000086

• MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model

  This is the DAC for the study "MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model" of Pavlo Lutsik (DKFZ B370/KU Leuven, pavlo.lutsik@kuleuven.be) and Clarissa Gerhauser (DKFZ B370, c.gernauser@dkfz.de)

  Dac EGAC50000000497

• Long-read whole genome sequencing as a tool for variant detection in inherited retinal dystrophies

  WGS sequencing using nanopore long reads sequencing. These data is used for the diagnosis of patients with inherited retinal dystrophies.

  Study EGAS50000000846

• Gene expression by RNAseq in bronchial biopsies of asthmatics, asthma in remission and healthy subjects

  The study focus was differential expression in bronchial biopsies between persistent asthma, asthma in remission and healthy controls using RNAseq.

  Study EGAS00001003735

• ESGI___Whole_Genome_Sequencing_of_samples_from_the_INGI_Val_Borbera_genetic_isolate__X10_

  Whole genome sequencing of sampels from an isolated population from the Val Borbera valley in Italy. The samples are sequenced using the Illumina HiSeq X Ten system.

  Study EGAS00001001123

• DNA methylation in bronchial biopsies of asthmatics, asthma in remission and healthy subjects

  The study focus was differential methylation in bronchial biopsies between persistent asthma, asthma in remission and healthy controls using Illumina 450k arrays.

  Study EGAS00001003739

• Capture-based NGS

  Capture-based NGS obtained using the "all-CLL" panel (also known as SOPHiA DDM (TM) Community CLL Clonality Solution). Library preparation was performed following SOPHiA GENETICS recommendations using 200 ng genomic DNA. Libraries were sequenced on a MiSeq instrument (2x300 bp, Illumina) aiming at a mean coverage of 1,000x.

  Dataset EGAD00001011151

• Whole exome sequencing of 3 primary Plasma Cell Leukemia samples

  Primary plasma cell leukemia (pPCL) samples were sequenced using the Nimblegen MedExome Plus hybridization capture to detect translocations, copy number changes, and mutations in 3 pPCL samples and patient matched controls. Sequencing was performed on a NextSeq500 using 75 bp paired end reads.

  Dataset EGAD00001005306

• HV31 - Bionano DLS optical mapping

  Bionano DLS optical mapping data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a molecule depth of ~153×. Optical mapping was performed at the Weatherall Institute of Molecular Medicine using the Bionano Saphyr platform.

  Dataset EGAD00001007049