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From GWAS to PheWAS: Scanning the EMR Phenome for Gene-disease Associations

ABSTRACT: From GWAS to PheWAS: Scanning the EMR Phenome for Gene-disease Associations

PROVIDER: PRJNA428409 | ENA |

REPOSITORIES: ENA

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From GWAS to PheWAS: Scanning the EMR Phenome for Gene-disease Associations

Project description:From GWAS to PheWAS: Scanning the EMR Phenome for Gene-disease Associations

| PRJNA428408 | ENA

Next generation sequencing facilitates quantitative analysis of Caenorhabditis elegans N2 wild type, emr-1(gk119), lem-2(tm1582) and emr-1(RNAi) lem-2(tm1582) transcriptomes.

Project description:Laminopathies are caused by mutations in components of the nuclear envelope (NE). While most NE components are widely expressed, laminopathies affect only a subset of tissues. However, the understanding of the molecular mechanisms that explain this phenomenon is still elusive. Here we have performed RNA-Seq analysis in adult C. elegans nematodes comparing gene expression in wild type and single and double mutants of two components of the NE, EMR-1 and LEM-2. Our data confirm that EMR-1 and LEM-2 facilitate gene repression and that both proteins control the expression of mainly muscle and neuronal genes. mRNA profiles of wild type, emr-1(gk119), lem-2(tm1582) and emr-1(RNAi) lem-2(tm1582) young adult worms were generated by deep sequencing, in triplicate for the wild type and duplicates for the other backgrounds, using Illumina GAIIx.

2013-12-02 | E-GEOD-44682 | biostudies-arrayexpress

DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms

Project description:Laminopathies are caused by mutations in components of the nuclear envelope (NE). While most NE components are widely expressed, laminopathies affect only a subset of tissues. However, the understanding of the molecular mechanisms that explain this phenomenon is still elusive. Here we have performed a genome wide DamID analysis in adult C. elegans nematodes comparing the DNA association profile of two components of the NE, Lamin/LMN-1 and Emerin/EMR-1. Although both proteins were associated to silent DNA, EMR-1 showed a predominant role in the anchoring of muscle and neuronal promoters to the nuclear periphery. Deletion of either EMR-1 or LEM-2, another integral NE protein, caused local changes in nuclear architecture with both increased and decreased LMN-1 association.

2013-12-02 | GSE44188 | GEO

Next generation sequencing facilitates quantitative analysis of Caenorhabditis elegans N2 wild type, emr-1(gk119), lem-2(tm1582) and emr-1(RNAi) lem-2(tm1582) transcriptomes.

2013-12-02 | GSE44682 | GEO

Phenome analysis of Mycoplasma pneumoniae

Project description:Phenome analysis of Mycoplasma pneumoniae

| PRJEB10038 | ENA

DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms

Project description:Laminopathies are caused by mutations in components of the nuclear envelope (NE). While most NE components are widely expressed, laminopathies affect only a subset of tissues. However, the understanding of the molecular mechanisms that explain this phenomenon is still elusive. Here we have performed a genome wide DamID analysis in adult C. elegans nematodes comparing the DNA association profile of two components of the NE, Lamin/LMN-1 and Emerin/EMR-1. Although both proteins were associated to silent DNA, EMR-1 showed a predominant role in the anchoring of muscle and neuronal promoters to the nuclear periphery. Deletion of either EMR-1 or LEM-2, another integral NE protein, caused local changes in nuclear architecture with both increased and decreased LMN-1 association. Comparison of Dam::LMN-1 and Dam::EMR-1 DNA assotiation in wild type strains and Dam::LMN-1 DNA association in wild type, lem-2(tm1582) and emr-1(gk119) mutant backgrounds.

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Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells (RNA-seq)

Project description:Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. Despite the abundance of GWAS associations, functional identification and characterization of causative variants and effector genes remains a challenging prospect. Human erythropoiesis provides a highly tractable model system for the development of tools for GWAS analysis. Using the Human Umbilical Derived Erythroid Progenitor 2 (HUDEP-2) cell line we have modelled the effects of two variants associated with red blood cell traits using CRISPR/Cas9 facilitated HDR editing.

2023-01-21 | GSE125714 | GEO

Modelling of Red Blood Cell Trait GWAS Variants in HUDEP-2 Cells (ChIP-seq)

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ChIP-seq H3K4me3 on sperm from FVB/NCrl-Trim66em2(gfp)Emr

Project description:ChIP-seq H3K4me3 on sperm from FVB/NCrl-Trim66em2(gfp)Emr and wild type mice

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