ChIFITM variants
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ABSTRACT:
PROVIDER: PRJEB30616 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Re-sequencing of the chicken IFITM locus using PacBio sequencing technology.
| PRJEB19334 | ENA
Project description:Re-sequencing of the chicken IFITM locus using PacBio sequencing technology.
| PRJEB19260 | ENA
Project description:Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we used seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in three disease-relevant immune cell types, based on a set of features related to regulatory potential. Trait/disease-associated variants were enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 had at least one variant meeting one or both of these criteria, with 3 of these haplotypes having a single prioritized variant. 5 of the 9 prioritized variants were further supported by genetic fine-mapping in our and other studies. Our work provides evidence for the efficacy and limitations of strategies for prioritizing disease- and trait-associated genetic variants.
2020-02-11 | GSE136686 | GEO
Project description:We performed an analysis of 489 GWAS variants that are associated with RA disease or are markers of RA drug efficacy. These variants were analyzed for: 1) their spatial interactions in three-dimensions, as captured by proximity ligation; 2) chromatin markers of regulatory functions (DNAse Hypersensitivity Sites, transcription factor binding site motifs, luciferase allele-specific SNP enhancer activity); and 3) their ability to affect linked gene expression (i.e. act as an eQTL). SNPs rs3184504, rs653178, and rs11545078 show evidence of differential long distance spatial associations in HL-60/S4 cells in undifferentiated versus differentiated cell states. RA associated variants at the SH2B3 locus (rs3184504/rs653178)) have a spatially-reinforced eQTL with BAZ2A, ~60Mb away, which affects platelet formation. Similarly, a variant at the GGH locus, which is associated with methotrexate toxicity, forms an inter-chromosomal spatially-reinforced eQTL with MGEA5, which is overexpressed in peripheral blood mononuclear cells.
2019-12-01 | GSE101812 | GEO
Project description:There are six histone H1 variant in chicken. 01H1/02H1/03H1/.10H1/H1L and H1R. In those variant we forcused on H1L and H1R those molecule were most similar H1 among six H1 variants. we established linker histone H1L and H1R deleted mutant in chicken B-cell derived DT40 cell and assay gene expression in normal condition in those mutant cells. The detail charactalization of those mutant cell was published in Takami et al., BBRC 268, 501-508 (2000) and Hashimoto et al., DNA repair (in press) Experiment Overall Design: There are six linker histone H1 variant in chicken. Linker histone was thought to be general gene supplesser. We established linker histone H1 variant mutant in chicken B-cell derived DT40 cell, and analyze total protein by 2D-PAGE to find up- or down- regulatd protein. In these mutant, there are some up regulated protein expression and down regulated protein expression (Takami et al., BBRC 268, 501-508 (2000), PubMedID 10679234). Experiment Overall Design: These 2D-PAGE experiment were limited at low density protein region, we use Affymetrix array to search the gene that were regulated specific linker histone H1 variant mutant. Experiment Overall Design: We assayed total gene expression profile in H1L and H1R deleted mutant cells. Experiment Overall Design: all mutant cells were cultured in normal culture condition in RPMI 1640 medium supplemented with 10 µM 2-mercaptoethanol, 10% FCS (Biowest) and 1% chicken serum (Gibco) at 39.5ËC. Total RNA were isolated from exponently growing DT40 cells.
2008-11-08 | E-GEOD-5114 | biostudies-arrayexpress
Project description:We used Affymetrix microarrays to understand the genome wide differences in gene expression between WT and Ifitm-/- CD4 T cells
2019-03-18 | GSE90494 | GEO
Project description:Isolates of Cryptococcus neoformans, a fungal pathogen that kills almost 200,000 people worldwide each year, differ at a few thousand up to almost a million DNA sequence positions compared to a 19-megabase reference genome. We used bulked segregant analysis and association analysis, genetic methods that require no prior knowledge of sequence function, to address the key question of which naturally occurring variants influence fungal virulence. We identified a region containing such variants, prioritized them, and engineered strains to test our findings in a mouse model of infection. At one locus we identified a 4-nt variant in the PDE2 gene, which severely truncates its phosphodiesterase product and significantly alters virulence. Our studies demonstrate a powerful and unbiased strategy for identifying key genomic regions in the absence of prior information, suggest revisions to our assumptions about cAMP levels and about common laboratory strains, and provide significant sequence and strain resources to the community.
2023-10-23 | GSE232437 | GEO
Project description:Despite significant progresses, the genetic roles of regulatory elements in gene expression still remain largely unknown in prostate cells. Recent development in single cell sequencing has made it possible to combine ATAC-seq and RNA-seq to determine genome-wide linkages between chromatin accessibilities and gene expression. To test the feasibility of using single cell multiome sequencing in dissecting regulatory linkages between chromatin accessibilities and gene expressions, we applied 10X Multiome ATAC + Gene Expression platform to simultaneously encapsulate Tn5 transposase tagged nuclei from multiple prostate cell lines. Based on these multiomic data, we developed subsampling linkage analysis to identify linkage associations between open chromatin and gene expressions. Moreover, we implemented an innovative analytical method to investigate RNA expression alterations related to germline variant locus accessibilities at single cell levels, i.e., expression quantitate accessible loci (eQAL) analysis. Our data and methodology will complement traditional eQTL analysis and foresee more genetic applications aiming to clarify regulatory elements by single cell sequencing.
2024-07-31 | GSE264518 | GEO