14983 results for "cancer studies using rna-seq"

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• RNA-seq explants chondrocytes

  Osteochondral explants were obtained from knee joints (n=17 explants) from the RAAK study. Paired-end 2x150 bp RNA sequencing (Illumina TruSeq mRNA Library Prep Kit, Illumina HiSeq X) was performed.

  Dataset EGAD00001008752

• Cardiac Translatomes of 80 Human Samples

  Dataset consists of fastq files of Ribo-seq, polyA-RNA and total RNA sequencing of 80 samples (65 DCM cases and 15 controls)

  Dataset EGAD00001004394

• RNA seq of MPNST tumour samples

  RNA sequencing of 10 MPNST tumour samples as part of a larger study of MPNST. Article: Lyskjær et al, 2020, J Pathol, "H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours".

  Study EGAS00001004528

• Human embryonic stem cells dopaminergic neurons scRNA-seq

  The dataset includes 2 samples of Single cell RNA-seq (10X Genomics) from Human Embryonic stem cells. 2 samples with 2 replicates of timepoints 17 and 28 of dopaminergic neuron differentiation.

  Dataset EGAD50000001592

• scMultiome

  This dataset gather scMultiomic data including RNA-seq and ATAC-seq in MM.1S in control and dex condition at 1h and 4h

  Dataset EGAD00001011140

• PsychENCODE Consortium: Epigenetic and Transcriptional Dysregulation in Autism Spectrum

  Our current understanding of autism spectrum disorders (ASD) delineates a highly heritable, yet etiologically heterogeneous disease. Forward genetic approaches to find disease associated mutations or common variation have been successful and continue to offer considerable power. Yet, given the accumulating evidence for very significant heterogeneity and environmental influences, complementary approaches to classic forward genetics become necessary. Genetic polymorphism and mutation data to date have identified dozens of causal or contributory variants, yet our preliminary data from autism brain suggest that common molecular pathways are involved in a significant subset of cases. This convergence at the tissue level suggests that other mechanisms, specifically epigenetic changes, combined with genetic background, are contributing to such final common pathways. We further tested this hypothesis by taking a comprehensive and integrative genome-wide approach to assessing brain gene-expression, miRNA levels and the related, causal epigenetic mechanisms in ASD etiology. We performed RNA-seq analyses of four cerebral cortical regions and cerebellum from ASD cases and controls, to assess mRNA, miRNA, and splicing isoform regulation. In parallel, we identified key differences in chromatin state and DNA methylation across multiple brain regions in the same ASD and control individuals used in the expression analyses using ChIP-Seq and MeDIP. We assessed the mechanisms by which changes in DNA methylation, histone modification, and DNA sequence contribute to the observed differences in gene expression. This work, which represents an unprecedented effort to unify these often disparate data (usually produced without integration in mind), delineates potential shared molecular pathways in ASD and the underlying mechanism of these differences at the level of miRNA, the chromatin regulatory apparatus, and DNA methylation. The following substudies are part of the PsychENCODE release at dbGaP and offer additional molecular data: PsychENCODE: RNA-Sequencing - SRRM4 Splicing Study phs000872 PsychENCODE: Global Changes in Patterning, Splicing and lncRNAs phs001061 PsychENCODE: Chromatin Contact Map in Fetal Cortical Laminae phs001190 PsychENCODE: Epigenetic Dysregulation in Autism Spectrum Disorder phs001220

  Study phs001022

• Baulac Lab - Paris Brain Institute

  Raw 10X single-nucleus RNA-seq data from human postoperative brain samples of patients with epilepsy and cortical malformations.

  Dac EGAC50000000546

• Transcriptomic profiling of lymphedema

  RNA-seq of skin from human subjects with and without lymphedema

  Dataset EGAD00001006246

• Population Architecture using Genomics and Epidemiology (PAGE)

  PAGE II (2013-2017) seeks to expand understanding gained during PAGE I and similar studies of how ancestry-specific differences in allele frequencies and LD may explain differences in risks of common traits and conditions. Recent studies have identified rare genetic variants that are likely to contribute to common diseases and traits and observed that rare variants likely to be functional, such as those in coding and regulatory regions, tend to be population-specific. PAGE II has genotyped over 50,000 samples using MEGA, an Illumina high density custom exomechip array. The MEGA data is being imputed in PAGE to the 1000 Genomes panel. PAGE also sequenced 1,000 samples representative of 21 populations from the Americas. PAGE has harmonized phenotype data for ~300 trait variables. These datasets will be analyzed to continue emphasis on characterizing population-level disease risks in non-European-descent individuals. Cohorts in PAGE II are: CALiCo (Causal Variants Across the Life Course, a consortium of ARIC, CARDIA, HCHS/SOL, Strong Heart Studies), ISMMS (Mount Sinai BioMe Biobank), MEC (Multiethnic Cohort), WHI (Women's Health Initiative), and Stanford University (PAGE Global Reference Panel). Genotyping services were provided by the Center for Inherited Disease Research (CIDR) and sequence data were provided by the McDonnell Genome Institute at Washington University School of Medicine. PAGE I (2008-2013): The first phase of PAGE examined putative causal genetic variants across approximately 100,000 African Americans, Asian Americans, American Indians, European Americans, Hispanic Americans, and Native Hawaiians from four groups representing nine large U.S.-based cohorts. Two genotyping approaches were employed - targeted genotyping of selected SNPs identified in genome-wide association studies of common disease, and a large-scale effort focused on the Metabochip array, which facilitated trans-ethnic fine mapping of several diseases of public health importance. Cohorts in PAGE I were: CALiCo (Causal Variants Across the Life Course, a consortium of ARIC, CARDIA, CHS, HCHS/SOL, Strong Heart Cohort Study, Strong Heart Family Study), EAGLE (Epidemiologic Architecture for Genes Linked to Environment, based on 3 National Health and Nutrition Examination Surveys (NHANES)), MEC (Multiethnic Cohort) and WHI (Women's Health Initiative). Logistical and scientific support is provided by the PAGE Coordinating Center and the NHGRI Division of Genomic Medicine. PAGE II is funded by the NHGRI and the NIMHD. To access PAGE studies currently available in dbGaP, please click on the links below.Please note that some PAGE studies belong to larger cohorts and have been included as PAGE substudies. For those studies, there is an additional link to the parent study. phs000223 PAGE-ARIC and phs000280 ARIC Cohort phs000236 PAGE-CARDIA and phs000285 CARDIA Cohort phs000301 PAGE-CHS and phs000287 CHS Cohort phs000559 PAGE-EAGLE-BioVu phs000208 PAGE-EAGLE-NHANES phs000555 PAGE-HCHS/SOL and phs000810 HCHS/SOL Cohort phs000220 PAGE-MEC phs000580 PAGE-SHS and SHFS phs001033 PAGE Global Reference Panel phs000227 PAGE-WHI and phs000200 WHI Cohort

  Study phs000356

• DNA Methylation Analysis of Prostate Cancer Cell Lines and Tissues Using Next Generation Sequencing

  Aberrant DNA methylation changes are known to occur during prostate cancer progression beginning with precursor lesions. Utilizing fifty nanograms of genomic DNA in Methylplex-Next Generation Sequencing (M-NGS) we mapped the global DNA methylation patterns in prostate tissues (n=17) and cells (n=2). Peaks were located from mapped reads obtained in each sequencing run using a Hidden Markov Model (HMM)-based algorithm previously used for Chip-Seq data analysis(http://www.sph.umich.edu/csg/qin/HPeak). The total methylation events in intergenic/intronic regions between benign adjacent and cancer tissues were comparable. Promoter CGI methylation gradually increased from -12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues and approximately 20% of all CpG islands (CGIs) (68,508) were methylated in tissues. We observed distinct patterns in promoter methylation around transcription start sites, where methylation occurred directly on the CGIs, flanking regions and on CGI sparse promoters. Among the 6,691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer specific and several previously studied targets were among them. A novel cancer specific DMR in WFDC2 promoter showed 77% methylation in cancer (17/22), 100% methylation in transformed prostate cell lines (6/6), none in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested a role for DNA methylation in alternate transcription start site utilization. While methylated promoters containing CGIs had mutually exclusive H3K4me3 modification, the histone mark was absent in CGI sparse promoters. Finally, we observed difference in methylation of LINE-1 elements between transcription factor ERG positive and negative cancers. The comprehensive methylome map presented here will further our understanding of epigenetic regulation of the prostate cancer genome. Overall Design: We mapped the global DNA methylation patterns in prostate tissues (n=17) and cells (n=2) from fifty nanograms of genomic DNA using Methylplex-Next Generation Sequencing (M-NGS). For replicate analysis in cell lines, a total of 4 runs were completed for PrEC prostate normal cell line, and 5 runs were completed for LNCaP prostate cancer cell line. For tissue samples, 2 benign prostate samples were sequenced twice on Illumina next generation sequencing platform to access overall repeatability of M-NGS.

  Study phs000597

• Pulmonary atypical carcinoid multi-omic dataset on up to 42 tumours from same patient

  Pulmonary atypical carcinoid. DNA WES and RNA-Seq on 42 tumour samples collected at autopsy, 10x Chromium linked read whole genome sequencing on four tumours plus one normal sample, and targeted DNA sequencing on two clinical biopsies and one blood plasma sample. Note – RNA-Seq dataset features complex batch effect attributable to tissue processing artefacts, as described in "Complex patterns of genomic heterogeneity identified in 42 tumor samples and ctDNA of a pulmonary atypical carcinoid patient" - Robb et al., 2022 and detailed in Supplementary Table S3. Note – RNA-Seq dataset features complex batch effect attributable to tissue processing artefacts, as described in "Complex patterns of genomic heterogeneity identified in 42 tumor samples and ctDNA of a pulmonary atypical carcinoid patient" - Robb et al., 2022 and detailed in Supplementary Table S3.

  Dataset EGAD00001009296

• Chondrosarcoma_Targeted_Sequencing_Study

  This Study uses a focused bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these finding in a larger set of patients.

  Study EGAS00001000277

• Sequencing of longitudinal glioma pairs

  Clonal evolution drives cancer progression and therapeutic resistance. Recent studies revealed divergent longitudinal trajectories in gliomas, but early molecular traits steering post-treatment cancer evolution remain unclear. We analyzed sequencing data of 544 initial-recurrent adult diffuse glioma pairs to identify genomic and transcriptomic early predictors of tumor evolution in each molecular subtype.

  Dataset EGAD00001009845

• Dataset for RNA sequencing glioblastoma data

  This dataset contains RNA sequencing data of 36 glioblastoma samples. Sequencing was performed on Illumina NovaSeq 6000 using TruSeq Stranded RNA Kit. The sequencing was always paired.

  Dataset EGAD50000000688

• Single nucleus and bulk transcriptomics in prefrontal cortex of individuals with alpha synucleinopathies

  We explore cell-specific changes in gene expression across different α-synucleinopathies. We perform single nucleus RNA sequencing using 10X Genomics, and bulk RNA sequencing from the prefrontal cortex of individuals with alpha synucleinopathies - Parkinson's Disese (PD), monogenic LRRK2 PD, and multiple system atrophy (MSA), together with neurologically healthy controls.

  Study EGAS50000000301