Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1020967 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genotyping SAX1 Mouse Human Hybrid to identify haplotypes of chromosomes 7 and X
2010-08-27 | GSE23816 | GEO
Project description:The global transcriptional responses of the adult potato psyllid gut upon infection of the two Candidatus Liberibacter solanacearum (Lso) haplotypes using Illumina sequencing
2022-06-27 | GSE206877 | GEO
Project description:Shrub willow (Salix spp.), a short rotation woody biomass crop, has superior properties as a perennial energy crop for the Northeast and Midwest US. However, the insect pest potato leafhopper Empoasca fabae (Harris) (PLH) can cause serious damage and reduce yield of susceptible genotypes. Currently, the willow cultivars in use display varying levels of susceptibility under PLH infestation. However, genes and markers for resistance to PLH are not yet available for marker-assisted selection in breeding. In this study, transcriptome differences between a resistant genotype 94006 (S. purpurea) and a susceptible cultivar ‘Jorr’ (S. viminalis), and their hybrid progeny were determined. Over 600 million RNA-Seq reads were generated and mapped to the Salix purpurea reference transcriptome. Gene expression analyses revealed the unique defense mechanism in resistant genotype 94006 that involves PLH-induced secondary cell wall modification. In the susceptible genotypes, genes involved in programed cell death were highly expressed, explaining the necrosis symptoms after potato leafhopper feeding. Overall, the discovery of resistance genes and defense mechanisms provides new resources for shrub willow breeding and research in the future.
2020-01-15 | GSE143616 | GEO
Project description:We adapted the widely used digestion of chromatin with micrococcal nuclease (MNase) followed by deep sequencing to the parasite Trypanosoma cruzi, which presents numerous singularities. In this work, we use the hybrid CL Brener strain carrying two set of chromosomes from two substantially different parental strains. The hybrid strain CL Brener is composed of the Esmeraldo-like and non Esmeraldo-like haplotypes. Additionally, part of the genome was not assembled into any of the haplotypes. Sometimes the community working in the field uses just one haplotype as reference genome for simplicity. In this work, we emphasize the importance of using its whole genome as a reference. Moreover, we extended our analysis to a clonal strain, Sylvio-X10.
2023-10-23 | GSE176341 | GEO
Project description:Genotyping SAX1 Mouse Human Hybrid to identify haplotypes of chromosomes 7 and X Single sample prepared from SAX1 cells
2010-08-27 | E-GEOD-23816 | biostudies-arrayexpress
Project description:Small RNAs, including microRNAs (miRNAs), phased secondary small interfering RNAs (phasiRNA), and heterochromatic small interfering RNAs (hc-siRNA) are an essential component of gene regulation. To establish a broad potato small RNA atlas, we constructed an expression atlas of leaves, flowers, roots, and tubers of Desiree and Eva, which are commercially important potato (Solanum tuberosum) cultivars. All small RNAs identified were observed to be conserved between both cultivars, supporting the hypothesis that small RNAs have a low evolutionary rate and are mostly conserved between lineages. However, we also found that a few miRNAs showed differential accumulation between the two potato cultivars, and that hc-siRNAs have a tissue specific expression. We further identified dozens of reproductive and non-reproductive phasiRNAs originating from coding and noncoding regions that appeared to exhibit tissue-specific expression. Together, this study provides an extensive small RNA profiling of different potato tissues that might be used as a resource for future investigations.
2022-11-11 | GSE213986 | GEO
Project description:The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments. Keywords: experiment with factorial design
2009-02-02 | GSE11875 | GEO
Project description:The cultivar Desirée and the breeding line SW93-1015 were challenged with potato cyst nematodes and transcriptomes analysed after 8h and 48 h.
2018-04-02 | E-MTAB-5215 | biostudies-arrayexpress
Project description:Environmental isolates of Vibrio cholerae from California coastal water compared to reference strain N16961. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design; array CGH
2007-07-17 | GSE8499 | GEO
Project description:The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments. Keywords: experiment with factorial design factorial design; 2 potato cultivars (Sante, Lady Balfour); 2 fertilizers (dairy manure compost, chicken manure pellets); 3 plant protection treatments (copper oxychloride, comcat, water), 3 biological replicates, 48 samples
2009-02-01 | E-GEOD-11875 | biostudies-arrayexpress