Ontology highlight
ABSTRACT:
PROVIDER: PRJNA416289 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This experiment was carried out in the context of a whole-genome sequencing study in 4 affected and 4 unaffected relatives of a consanguineous Italian family characterized by the high prevalence of multiple sclerosis. These data were used to evaluate differences in GRAMD1B gene expression in whole blood comparing healthy and affected subjects of the family. Functional experiments have been subsequently performed to evaluate the involvement of this gene in multiple sclerosis.
2018-08-01 | GSE103005 | GEO
Project description:Multiple Sclerosis (MS) is known to be caused by a genetic predisposition triggered by environmental factors. Despite the knowledge of genetic factors and environmental agents involved, it is largely unclear how they interact. Epigenetics, particularly DNA methylation, represents a model for environmental factors to influence the genome. In this paper, we studied 26 affected and 26 unaffected relatives from 8 MS multiplex families (≥ 3 affected relatives) as part of a multicentric Italian cohort study using Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) run on an Illumina® HiSeq 2500 (2x100 bp). Technical validation in 6/8 of the original families and biological replication in 2 additional families (FDR < 0.1 and a concordant fold change, FC) were performed in suggestive differentially methylated regions (DMRs) between affected and unaffected relatives using SeqCap Epi Choice Enrichment (Roche®). Evidence of association from MeDIP-Seq across 8 families was combined with aggregation statistics, separately for hypo- and hyper-methylated regions with concordant FC in ≥ 6/8 families, yielding 162 DMRs at FDR ≤ 0.1. Technical validation and biological replication led to 2 hypomethylated regions, which point to NTM and BAI3 genes, and 2 hypermethylated regions in PIK3R1 and CAPN13 (mean size: 3.1 kb). Multiplex families represent a privileged setting for the study of regions of differential methylation as they reduce the impact of potential confounders like shared genetics and environmental factors. We identified 4 novel regions which contain genes of potential interest that need to be tested in larger cohorts of patients.
2021-05-01 | GSE149562 | GEO
Project description:Nabiximols treatment in Multiple Sclerosis patients
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Project description:Characterization of the mutational landscape of the 5T murine models for multiple myeloma, by whole-exome sequencing.
2018-10-09 | E-MTAB-5282 | biostudies-arrayexpress
Project description:Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.
2016-05-17 | E-ERAD-37 | biostudies-arrayexpress
Project description:Gut dysbiosis in patients with multiple sclerosis
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Project description:We generated induced pluripotent stem cells (iPSCs) of two patients with Tetralogy of Fallot (TOF) and three healthy relatives of two unrelated familes. We furhter performed mRNA sequencing of iPSCs (day 0) and derived cardiomyocytes (CMs) at day 15 and 60 of patients and healthy relatives.
2020-06-19 | GSE111230 | GEO
Project description:While the next generation sequencing technology is accelerating the discovery of sites in RNA editing, the strategies to accurately identify the editome, the mechanism by which its profile is maintained and its functional significance remain controversial. Here, 90bp × 2, paired-end, strand-specific, polyA-postive RNA-Seq were performed in 3 rhesus monkey tissues, and 90bp × 2, paired-end, whole exome sequencing was performed in blood cells. Combining genome-wide identification and other quality control in multiple tissues from the same individual, we identified a list of editing sites in coding regions from the rhesus macaque, one of our closest evolutionary relatives. Low-scale verification validated all of these sites and the corresponding levels of editing. The editome in macaque coding region suggests RNA editing as a type of controlled, conserved regulation shaped by purifying selection. This submission represents RNA-Seq: cerebellum, lung, kidney and heart component of study.
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Project description:Whole exome sequencing identification of putative founder mutations in non-BRCA1/2 breast cancer patients
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