ABSTRACT: To comprehensively characterize the genetic structure of the Druze population, we recruited and genotyped 40 parent-offspring trios from the Upper Galilee in Israel and the Golan Heights, attempting to capture different extended families (clans) across various geographical locations.
Project description:Inferring the heritability of gene expression is one of the main areas of the field of genetical genomics. With the possibility to treat the abundances of gene transcripts as a suite of quantitative traits, genetical genomics can make an extensive use of the microarray technology. Here we extended a major method for estimating the heritability of a quantitative trait, single parent-offspring regression, to assess the heritability of the expression of genes with two-channel microarrays. In a series of maternal parent-offspring pairs of Interior spruce (Picea glauca x engelmannii, our focus in the outer stem tissues is the expression of defense-related genes, the heritability of which can affect fitness and necessary for evolution by natural selection.
2010-07-15 | GSE22921 | GEO
Project description:Saffron Rhizosphere bacteriome from different geographical locations
Project description:Inferring the heritability of gene expression is one of the main areas of the field of genetical genomics. With the possibility to treat the abundances of gene transcripts as a suite of quantitative traits, genetical genomics can make an extensive use of the microarray technology. Here we extended a major method for estimating the heritability of a quantitative trait, single parent-offspring regression, to assess the heritability of the expression of genes with two-channel microarrays. In a series of maternal parent-offspring pairs of Interior spruce (Picea glauca x engelmannii, our focus in the outer stem tissues is the expression of defense-related genes, the heritability of which can affect fitness and necessary for evolution by natural selection. Parent-offspring pairs of Interior spruce planted as a part of Tree Breeding and Improvement Program of the Forest Genetics Section, British Columbia Ministry of Forests and Range, Prince George, BC, Canada (http://www.for.gov.bc.ca/hre/forgen/interior/spruce.htm#1) were used. A total of 30 trees, comprising 15 parent-offpsring pairs were sampled. These include15 offsprings and 15 maternal parents (grafts), which were planted within ~ 1Km range west (122º 42’ 43’’W, 53º 45’41’’N) of the offsprings, hence grown in a relatively similar environment. The bark and the attached phloem were separated from inner layers in the mid-morning hours of June 25, 2008, flash-frozen in liquid nitrogen, and transferred into separate containers. A chain design was decided for gene expression profiling (a total of 45 slides) using the Treenomix third generation cDNA microarray platform (GEO accession #: GPL5423). Array350 kit (Genisphere, Hatfield, USA) was chosen for the microarray hybridizations. The slides were scanned with a ProScanArray scanner (PerkinElmer, Downers Grove, IL, USA), and the scanned TIF images were processed by ImaGene software (BioDiscovery, Inc., El Segundo, CA, USA) to quantify spot signals. Normalization was done between arrays using variance stabilizing (VSN) method for ratio based analysis of the expression data.
Project description:Geographical distinct virulent Babesia bovis strains have similar gene expression changes as they go through attenuation. Pair end RNA-sequencing reads on three biological replicate sample pairs of virulent parent and attenuated derivative Babesia bovis strain isolated in Argentina.
Project description:It is becoming clear that copy number polymorphism in the human genome is a significant form of genetic variation. We have developed a new method that uses SNP genotype data from parent-offspring trios and applied it to HapMap to conduct high-resolution detection of deletion polymorphism. Of the delections uncovered, approximately 100 have been experimentally validated using comparative genome hybridization on these tiling-resolution oligonucleotide microarrays. We identified a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the parent-offspring trios. This new method will permit future identification of deletion polymorphisms from high density SNP data derived from parent-offspring trios or other family relationships. Keywords: comparative genomic hybridisation
Project description:Genome-wide methylation profiling on 15 Father-Mother-Offspring trios with Genetic Generalized Epilepsies. All trios have 2 affected (1 parent and offspring) and 1 healthy individuals. Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles which has probes for aproximetely 450000 CpG loci.
