Addictions: Genotypes, Polymorphisms, and Function/Human Genetic Correlates of Addictive Diseases
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ABSTRACT:
PROVIDER: PRJNA318658 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Addictions: Genotypes, Polymorphisms, and Function/Human Genetic Correlates of Addictive Diseases
| PRJNA318659 | ENA
Project description:Detection of single feature polymorphisms comparing five barley genotypes. Gene expression under unstressed and drought stressed conditions. Tissue from five entire five day old seedlings from drought stress or unstressed growth conditions was used for RNA extraction. For Barke, Morex and Stepoe the two types of RNA were pooled. For Oregon Wolfe Barley Dominant and Recessive (OWBs), the two types of RNA were handled separately. Targets from three biological replicates of each genotype-treatment were generated and transcript levels were determined using Affymetrix Barley1 GeneChip arrays. Probe set, followed by single probe, comparisons between genotypes allows the identification of single feature polymorphisms in comparisons between genotypes. For the OWBs, comparisons between stressed and unstressed conditions defines stress-regulated genes. Keywords: repeat
2005-08-25 | GSE3170 | GEO
Project description:Detection of single feature polymorphisms comparing five barley genotypes. Gene expression under unstressed and drought stressed conditions. Tissue from five entire five day old seedlings from drought stress or unstressed growth conditions was used for RNA extraction. For Barke, Morex and Stepoe the two types of RNA were pooled. For Oregon Wolfe Barley Dominant and Recessive (OWBs), the two types of RNA were handled separately. Targets from three biological replicates of each genotype-treatment were generated and transcript levels were determined using Affymetrix Barley1 GeneChip arrays. Probe set, followed by single probe, comparisons between genotypes allows the identification of single feature polymorphisms in comparisons between genotypes. For the OWBs, comparisons between stressed and unstressed conditions defines stress-regulated genes. Experiment Overall Design: Three genotypes, three replicates each. Two additional genotypes, two sets of three replicates each.
2008-06-12 | E-GEOD-3170 | biostudies-arrayexpress
Project description:Copy number variants (CNVs) can reach appreciable frequencies in the human population, and several of these copy number polymorphisms (CNPs) have been recently associated with human diseases including lupus, psoriasis, Crohn disease, and obesity. Despite new advances, significant biases remain in terms of CNP discovery and genotyping. Developing a novel method based on single channel intensity data and benchmarking against copy numbers determined from sequencing read-depth, we successfully obtained CNP genotypes for 1489 CNPs from 487 human DNA samples from diverse ethnic backgrounds. This customized microarray was enriched for segmental duplication-rich regions and novel insertions of sequences not represented in the reference genome assembly or on standard single nucleotide polymorphism (SNP) microarray platforms. We observe that CNPs in segmental duplications are more likely to be population differentiated than CNPs in unique regions (p = 0.015) and that bi-allelic CNPs show greater stratification when compared to frequency-matched SNPs (p = 0.0026). Although bi-allelic CNPs show a strong correlation of copy number with flanking SNP genotypes, the majority of multi-copy CNPs do not (40% with r >0.8). We selected a subset of CNPs for further characterization in 1873 additional samples from 62 populations (947 samples analyzed by microarray; 926 samples analyzed with PCR based assays); this revealed striking population-differentiated structural variants in genes of clinical significance such as the OCLN gene, a tight junction protein involved in hepatitis C viral entry. Our new microarray design allows these variants to be rapidly tested for disease association and our results suggest that CNPs (especially those that are not in linkage disequilibrium with SNPs) may have contributed disproportionately to human diversity and selection.
2011-02-01 | GSE26450 | GEO
Project description:Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, a dozen reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions. For most organisms, however, few or no such reference datasets are publicly available. Here, we describe a new type of datasets highly representative for the spatial, temporal and response dimensions of gene expression. They result from integrating expression data from a large number of globally normalized and quality controlled public experiments and aggregating results by anatomical parts, stages of development, perturbations, drugs, diseases, neoplasms, and genotypes. The proposed datasets were created for human and several model organisms and are publicly available at www.expressiondata.org.
2013-05-15 | GSE44938 | GEO
Project description:Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, a dozen reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions. For most organisms, however, few or no such reference datasets are publicly available. Here, we describe a new type of datasets highly representative for the spatial, temporal and response dimensions of gene expression. They result from integrating expression data from a large number of globally normalized and quality controlled public experiments and aggregating results by anatomical parts, stages of development, perturbations, drugs, diseases, neoplasms, and genotypes. The proposed datasets were created for human and several model organisms and are publicly available at www.expressiondata.org. PMI: 18 Samples were used with 2 different experimental factors: 1. 2 harvesting times (morning/afternoon) 2. 3 pos-harvesting times. 3 biological replicates were used.
2013-05-15 | E-GEOD-44938 | biostudies-arrayexpress
Project description:Interventions: The study will correlate the toxicity-adjusted dose of imatinib after 3 months of therapy with polymorphisms of drug elimination genes, particularly ABCB1 (MDR1). Patients will be asked to give a single blood sample for genotyping (at any time) and we will collect clinical data on dose and toxicity retrospectively from medical records.
Primary outcome(s): To determine whether ABCB1 genotype correlates with toxicity-adjusted dose of imatinib[At 3 months +/- 14 days]
Study Design: Purpose: Natural history;Duration: Cross-sectional;Selection: Defined population;Timing: Both
| 2452715 | ecrin-mdr-crc
Project description:Transcripcional responses in three genotypes of Muzus persicae, each exhibiting different resistance mechanisms, in response to an anti.cholinesterase insecticide
2013-01-01 | GSE37310 | GEO