Ontology highlight
ABSTRACT:
PROVIDER: PRJNA439358 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6872640_1.fastq.gz | Fastqsanger.gz | |||
| SRR6872640_2.fastq.gz | Fastqsanger.gz | |||
| SRR6872641_1.fastq.gz | Fastqsanger.gz | |||
| SRR6872641_2.fastq.gz | Fastqsanger.gz | |||
| SRR6872639_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
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Project description:Gene expression analysis of the epidermis from Lexicon Genetics Abca12 knockout mouse model of Harlequin Ichythois compared with wild type embryos to search for pathways specifically altered in the condition. Results indicate a large immune and inflammatory response occurs in the sterile environment of the uterus. Total RNA isolated from E17.5 back skin epidermis from murine Harlequin Ichthyosis model compared with wild type embryos.
2014-09-16 | E-GEOD-56125 | biostudies-arrayexpress
Project description:Congenital ichthyoses are rare and disabling genodermatoses caused by mutations in genes involved in the epidermal barrier. More than 60 genes are known to be involved. However, 5-10% of the genetic variants identified in those genes are rarely or not described and their pathogenicity not yet demonstrated. They are therefore classified as Variants of Uncertain Significance (VUS) that leave number of patients undiagnosed, precluding prognosis, counselling and treatment. We report here, an experimental strategy to reclassify VUS identified in congenital ichthyosis-causing genes tested for PNPLA1 variants. PNPLA is a transacylase essential for the skin barrier formation. It catalyzes the biosynthesis of acylceramides (AcylCer) in the stratum granulosum by esterification of ω-hydroxy ceramides with linoleic acid. We successfully characterized three PNPLA1 VUS identified in three patients with congenital ichthyosis, opening the possibility to extend the approach to other ichthyosis-causing genes.
2025-12-04 | GSE272321 | GEO
Project description:Gene expression analysis of the epidermis from Lexicon Genetics Abca12 knockout mouse model of Harlequin Ichthyosis compared with wild type embryos to search for pathways specifically altered in the condition. Results indicate a large immune and inflammatory response occurs in the sterile environment of the uterus.
2014-09-16 | GSE56125 | GEO
Project description:Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type — whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Through several case studies, we demonstrate how Exo-C's multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.
2024-01-24 | GSE253950 | GEO
Project description:<p>We investigated the cumulative contribution of rare, exonic genetic variants on the concentration of 1,487 metabolites and 53,714 metabolite ratios in urine by performing gene-based tests based on 226,233 variants from up to 4,864 participants of the German Chronic Kidney Disease (GCKD) study. There were 128 significant associations (53 metabolite-gene and 75 metabolite ratio-gene pairs) involving 30 unique genes, 16 of which are known to underlie recessively inherited inborn errors of metabolism (IEMs). Across the 30 genes, 47% of individuals carried at least one rare missense, stop or splice variant. The 30 genes were strongly enriched for shared high expression in liver and kidney (OR=65, p-FDR=3e-7), with hepatocytes and proximal tubule cells as driving cell types. Use of whole-exome sequencing data in the UK Biobank allowed for linking genes to diseases that could plausibly be explained by the identified metabolites. In silico constraint-based modeling of knockouts of the implicated genes in a virtual whole-body, organ-resolved metabolic human correctly predicted the observed direction of metabolite changes in urine and blood, highlighting the potential of linking population genetics to modeling to validate associations and to predict metabolic consequences of yet unknown IEMs. Our study extends the map of genes influencing urine metabolite concentrations, reveals metabolic processes and connected health outcomes, and implicates novel candidate variants and genes for IEMs.</p><p><br></p><p>Further links;</p><p><a href='https://www.gckd.org/' rel='noopener noreferrer' target='_blank'>German Chronic Kidney Disease (GCKD)</a></p>
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Project description:The biology of Harlequin Ichthyosis (HI), a devastating skin disorder, caused by loss of function mutations in the gene ABCA12, is poorly understood and to date no satisfactory treatment has been developed. We sought to investigate pathomechanisms of Harlequin Ichthyosis which could lead to the identification of safe and effective treatments to improve patients' quality of life. RNA-Seq analysis using normal skin (n=5) and HI patient skin (n=4) were performed to define the effects of loss of ABCA12. Functional annotation clustering analysis showed changes in three common groups: epidermal differentiation, lipid metabolism and inflammation (innate immunity and IFNγ signalling). In HI patient skin, gene expression of STAT1, STAT3 and Interleukin 36 (IL-36) A and G cytokines was significantly upregulated compared to normal skin, whereas IL-37, an inhibitor of innate immunity, was downregulated. RNA-Seq and functional assays were performed to define the effects of loss of ABCA12, using an engineered CRISPR-Cas9 ABCA12 KO 3D model. Functional annotation clustering analysis showed changes in three common groups: epidermal differentiation, lipid metabolism and inflammation.
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Project description:Autosomal recessive congenital ichthyoses (ARCI) are a group of non-syndromic congenital keratinization disorders including harlequin ichthyosis, lamellar ichthyosis, and congenital ichthyosiform erythroderma with a total prevalence of 1:200,000. Affected individuals who are often born as collodion babies present with generalized scaling of the skin. This reflects a physical compensation for the defective cutaneous permeability barrier underlying all ichthyoses. Inactivity of 12R-lipoxygenase (12R-LOX) is a frequent cause of ARCI. Epidermis-specific conditional knockout of Alox12b encoding 12R-LOX was established in mice using the Cre-Lox system. Tamoxifen-induced Alox12b inactivation in mouse skin caused an ichthyosis-like phenotype. We used microarray to compare the gene expression profile in the epidermis of mice after tamoxifen induced Alox12b inactivation with that of control animals. Inactivation of Alox12b was associated with the upregulation of genes involved in keratinization, cholesterol biosynthesis, and Fc-epsilon receptor signaling.
2019-03-01 | GSE127434 | GEO
Project description:CDAGS Syndrome is a rare congenital disorder characterized by Craniosynostosis, Delayed closure of the fontanelles, cranial defects, clavicular hypoplasia, Anal and Genitourinary malformations, and Skin manifestations. We performed exome sequencing to identify the underlying molecular cause in five patients with CDAGS syndrome from four distinct families. Whole exome sequencing revealed rare variants that disrupt highly conserved nucleotides within the RNU12 gene. RNU12 encodes a small nuclear RNA that is a component of the minor spliceosome and is essential for minor intron splicing. Targeted sequencing confirmed allele segregation within the four families. All five patients in this cohort have a rare variant on one allele that either disrupts the secondary structure or the Sm binding site of the RNU12 snRNA. The variant on the other allele, shared among all five cases, alters a highly conserved nucleotide within the precursor U12 snRNA 3’ extension that is absent in 1440 unrelated healthy controls. All of the variants are either rare or absent from all searched public databases. Whole transcriptome sequencing analysis identified gene dysregulation and specific defects in intron retention in a subset of minor intron splicing. These findings provide evidence of the involvement of RNU12 in craniosynostosis, anal and genitourinary patterning and cutaneous disease.
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Project description:We used whole exome sequence to identify de novo mutations in patients with ocular coloboma. Three of these encoded actin pathway components, ACTG1, TWF1 and LCP1. Mass spectrometry-based interactomes of wild-type and mutant proteins were performed to reveal altered functional interactions for all three variants.
2017-05-24 | PXD005090 | Pride