Customer-friendly solutions

- to complex problems

DNA sequencing and bioinformatics made easy
- we provide tailored sample-to-answer solutions

Custom projects

Besides our off the shelf products, DNASense offers made-to-measure solutions, customization of wetlab procedures and bioinformatics. Please find below a select list of examples, showcasing some of the custom projects that DNASense has undertaken. Contact us for a non-committal meeting to discuss your project idea and let’s together find a solution.

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Case 1: Gene Ontology (GO) over-enrichment analysis

Overenrichment analysis of overabundant Differentially Expressed Genes (DEGs) from an organism in response to change in carbon substrate supplement.

Several functional categories were found to be over-enriched among overabundant DEGs pertaining to phosphopanthetheine and purine ribonucleotide binding, respectively. Nodes that are statistical significantly overrepresented are colored green. Follow node arrows to identify highest possible functional classification (terminal end points).

The analysis can be performed on top of either RNA-Seq or proteomics data (DEGs) or even on complete genomes (CDS). Genes are called, Gene Ontology-characterized and overrepresented functional categories are identified. Functional networks can be inspected in Cytoscape afterwards.

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Case 2: Raw read taxonomic classification of metagenomes using Kaiju

Taxonomic classification of raw metagenomic sequencing reads (fastq) . In this pipeline fastq are processed and classified against all assembled and annotated genomes of archea, bacteria and vira from the NCBI RefSeq database, as well as proteins from fungi and microbial eukaryotes.

As indicated below, results are actionable and ideal for a quick survey of community structure. Can be appplied for both short-read (e.g. Illumina) and long read (e.g. ONT) sequencing data.

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Case 3: Linear discriminant analysis Effect Size (LEfSe)

LEfSe analysis was applied to identify significant changes in the microbial composition of mouse gut samples in response to antidepressant treatment. The identified differences are reported with their taxonomic assignment and their magnitude, the LDA score.

LEfSe can be applied as an add-on analysis on for our Microbial Community Analysis product (OTU/ASV) or genes or functions. The analysis requires replicates, which need to be included in the study design.

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