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:This study investigates the transcriptomic consequences of graded intracellular cyclic di-AMP (c-di-AMP) production in Mycobacterium bovis BCG Danish 1331. Wild-type BCG Danish 1331 (BCG-WT) was used as the parental reference strain. Two recombinant strains overexpressing the Mycobacterium tuberculosis diadenylate cyclase gene disA (Rv3586) were generated. In rBCG-V1, disA is expressed from the episomal plasmid pSD5-hsp60 under the control of the constitutive hsp60 promoter. rBCG-V2 carries an extrachromosomal recombinant plasmid, pKSB-hsp60-disA, containing two tandem copies of the hsp60-disA expression cassette, together with duplicated kanR and oriM sequences, while the chromosomal cdnP locus remains intact. These engineered strains generate progressively elevated intracellular c-di-AMP levels, with rBCG-V2 exhibiting higher c-di-AMP production than rBCG-V1. RNA sequencing was performed to characterize the global transcriptional changes associated with increasing c-di-AMP levels by comparing rBCG-V1 and rBCG-V2 with the parental BCG-WT strain.
Project description:Bulk RNA seq of FACS isolated C. elegans neurons, with pan-neuronal reference, and sorted viable cell reference samples. Collected for comparison to single cell sequencing data
Project description:Bulk RNA seq of FACS isolated C. elegans neurons, with pan-neuronal reference, and sorted viable cell reference samples. Collected for comparison to single cell sequencing data
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates Two color experiment, Escherichia coli Sakai (reference), clinical and environmental Escherichia coli strains (testers): At least two replicates including a single dye swap for each reference-tester comparison
Project description:In this study, we dissect in detail the glial and immune responses associated to early stages of CAA. To do so, RNAseq gene expression analysis were performed in a mouse model for Familial Danish Dementia (FDD), a neurodegenerative disease characterized by the accumulation of Danish amyloid (ADan) in the vasculature. Findings observed in this CAA mouse model were complemented with primary culture assays.
Project description:RNA analysis of 770 genes (Pan Cancer IO 360) related to the tumor microenvironment on NF1-MUT and matched NF1-WT samples for reference.
Project description:Structural genetic variants like copy number variants (CNVs) comprise a large part of human genetic variation and may be inherited as well as somatically acquired. Recent studies have reported the presence of somatically acquired structural variants in the human genome and it has been suggested that they may accumulate in elderly individuals. To further explore the presence and the age-related acquisition of somatic structural variants in the human genome, we investigated CNVs acquired over a period of 10 years in 86 elderly Danish twins as well as CNV discordances between co-twins of 18 monozygotic twin pairs. Furthermore, the presence of mosaic structural variants was explored.
