Project description:DNA was extracted from two ash tree samples, one tolerant and one susceptible to ash dieback. The DNA was sequenced using Nanopore technologies and the methylation was called against the new genome (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ) to identify differentially methylated regions between both samples. Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
Project description:A new genome of Fraxinus excelsior was assembled using a hybrid approach combining Nanopore and Illumina data (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ). Methylation was also assessed in the genome. Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
Project description:A new genome of Fraxinus excelsior (PRJNA865134) was assembled using a hybrid approach combining Nanopore and Illumina data. The gene expression of a 182 Danish tree panel (Harper et al. 2016) was assessed using the new genome as reference (BioProject PRJNA865134, SAMN30100368, genome JANJPF000000000 ).Manuscript title: Fraxinus excelsior updated long-read genome reveals the importance of MADS-box genes in tolerance mechanisms against ash dieback, G3:Genes|Genomes|Genetics
Project description:Purpose: this study provided a comprehensive sequence for a systemic view of the transcriptome between mango leaf and fruit, as well as fruit allergens, which will be useful for further genomic research studies and breeding of lower allergenic mango cultivars. Methods:Some allergens have previously been identified in mango (Mangifera indica Linn), including profilins, Bet v 1-like proteins and chitinase. In this paper, 66 potential allergen genes were identified and their relative expressions evaluated in mango fruit and leaf using Illumina RNA-Seq technology. Results:A total of 17.63Gb Clean Data was obtained.The number of %≥Q30 was above 94.58%.RNA-Seq generated 11,751,123 contigs that were assembled into 99,328 unigenes with 16,848 unigenes of >1000 bp. A total of 230,242 unigenes were annotated using public protein databases, with a cut-off E-value above 10−5, of which 27,295, 46,030, 24,227 and 14,023 unigenes were assigned to gene ontology terms, Nr, Swiss-Prot and clusters of orthologous groups, respectively. Allergens mainly belonged to pollen allergen, pathogenesis-related protein Bet v I family and NADPH-dependent FMN reductase.
Project description:Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the repeat units are longer than the sequence read length. To overcome this limitation, we have developed a TIS method using Oxford Nanopore sequencing technology that generates and uses long nucleotide sequence reads; we have called this method LoRTIS (Long Read Transposon Insertion-site Sequencing). This experiment data contains sequence files generated using Nanopore and Illumina platforms. Biotin1308.fastq.gz and Biotin2508.fastq.gz are fastq files generated from nanopore technology. Rep1-Tn.fastq.gz and Rep1-Tn.fastq.gz are fastq files generated using Illumina platform. In this study, we have compared the efficiency of two methods in identification of transposon insertion sites.
Project description:Here we developed a new approach to sepsis diagnosis that integrates host transcriptional profiling with metagenomic broad-range pathogen detection from cell-free plasma RNA and DNA.
Project description:Here we developed a new approach to sepsis diagnosis that integrates host transcriptional profiling with metagenomic broad-range pathogen detection from cell-free plasma RNA and DNA.