Genotyping of the PREDICT canola population by the Brassica 60K Illumina Infinium™ SNP genotyping array
Ontology highlight
ABSTRACT: 477 spring-type Brassica napus (canola) lines from a hybrid breeding programme were genotyped using the Brassica Infinium™ 60k genotyping array.
Project description:Clinical-grade human embryonic stem cells (hESCs) from 4 centres in the UK were cultured in self-renewal conditions Genomic DNA was isolated from low passage hESCs and submitted for SNP analysis using Illumina HumanCytoSNP-12 v2.1 BeadChip arrays Evaluation of molecular karyotype of multiple clinical-grade hESC lines.
Project description:Genomic imprinting is a mammalian-specific gene expression regulation system that distinguishes two parental alleles and yields parent-origin-specific gene expression. It has been identified approximately 90 imprinted gene loci in the mouse genome thus far. One of the molecular bases that establish genomic imprinting is through endogenous antisense transcription. In several imprinted loci, antisense transcription is observed in a repressive allele, probably contributing to the parent-origin-specific gene expression establishment. We investigated the allele- and strand-specific transcriptional dynamics of a megabase-wide genomic region of mouse Ube3a (ubiquitin protein ligase E3A), which is maternally expressed in a tissue-specific manner, by means of a highly parallel SNP genotyping platform that targets the tissue transcriptome. We successfully observed higher resolution transcriptional activity in the vicinity, including brain-specific widespread antisense transcription. We have listed up SNP sites within Ube3a-Snurf/Snrpn region between C57BL/6J and MSM/Ms. SNP sites were loaded onto Illumina GoldenGate Assay platform, and were assayed by targeting total RNA came from brain and liver of F1 hybrid mice.
Project description:Growth curves wt and hns strains in rich dYT medium. Sample in Mid-exponential phase (ME), Transition to Stationary (TS) and Late Stationary phase (LS).
Project description:The presence of a coding variant affecting plasma high density lipoprotein cholesterol (HDLC) levels was evaluated in subjects with elevated plasma levels of HDLC. 18 DNA samples from subjects with high plasma HDLC levels were analyzed. The samples were analyzed using the exome chip in three separate phases, with different samples in each phase. The same genotyping platform was used for each of the phases of the experiment under the same experimental conditions. Because different samples were run in different phases, raw intensity data was collected separately for each phase and genotypes were called separately for each phase. Raw intensity data is provided thus separately for the subjects by phase of genotyping. The experimental phase of each subject is also provided.
Project description:Effect of FIS and H-NS on gene expression at relexed and hypernagative supercoiling level using LZ41 and LZ54 strains. LZ41 and LZ54 strains contain drug-resistant alleles of different topoisomerase genes. LZ41 strain treatment norfloxacin strongly relaxes DNA, whereas in LZ54 strain the same treatment generates high negative supercoiling (Khodursky et al., 1995, PNAS 92:11801-5; Ziechedrich et al, 1997, Genes Dev. 11:2580-92).
Project description:Effect of supercoiling level on gene expression using LZ41 and LZ54 strains containing drug-resistant alleles of different topoisomerase genes. LZ41 strain treatment with norfloxacin strongly relaxes DNA, whereas in LZ54 strain the same treatment generates high negative supercoiling (Khodursky et al., 1995, PNAS 92:11801-5; Ziechedrich et al, 1997, Genes Dev. 11:2580-92).
Project description:Degenerative myelopathy (DM) is a canine disease very similar to amyotrophic lateral sclerosis (ALS) in humans. We previously showed that DM is a promising model for ALS, as genome-wide association identified a mutation in SOD1, a known ALS gene. In this study, we identify a modifier gene, SP110, which strongly affects overall disease risk and age-of-onset in Pembroke Welsh corgis at risk of DM. Dissecting the complex genetics of this disease in a model organism may lead to new insights about risk and progression in both canine and human patients. 15 DM-affected and 31 unaffected PWC homozygous for SOD1 mutation genotyped using the Illumina CanineHD array (~170,000 SNPs genomewide)
Project description:Degenerative myelopathy (DM) is a canine disease very similar to amyotrophic lateral sclerosis (ALS) in humans. We previously showed that DM is a promising model for ALS, as genome-wide association identified a mutation in SOD1, a known ALS gene. In this study, we identify a modifier gene, SP110, which strongly affects overall disease risk and age-of-onset in Pembroke Welsh corgis at risk of DM. Dissecting the complex genetics of this disease in a model organism may lead to new insights about risk and progression in both canine and human patients. 15 DM-affected and 10 unaffected Boxers homozygous for SOD1 mutation genotyped using the Illumina CanineHD array (~170,000 SNPs genomewide)
Project description:Familial thyroid cancer originating from follicular cells accounts for 5-15% of all the thyroid carcinoma cases in humans. Previously, we described thyroid follicular cell carcinomas in a large number of the Dutch German longhaired pointers (GLPs) with likely an autosomal recessive inheritance pattern. Here, we investigated the genetic causes of the disease using a combined approach of genome-wide association study, selective sweep analysis, and ROH analysis based on 170k SNP array genotype data. A region 0-5 Mb on chromosome 17 harboring the TPO gene was identified to be associated with the disease.