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We introduced FAQ page with useful information on NGS applications, project set up, data analysis and more.

Human DNA contamination in 16S rRNA gene sequence analysis

16S rRNA sequencing is fast and cost-effective approach used to investigate microbiome communities, yet it suffers some inefficiencies. The major problem encountered is eukaryotic host contamination, i.e. >80% of 16S reads can be wasted due to off target amplification from the host’s genome. While this problem is well known to those who work with plants, it seems to be underestimated in the human sector.

Sustainable Agriculture: Role of Metagenomics in Exploring the Soil Microbiota

The implementation of the EU Farm to Fork Strategy will require an environmentally-friendly utilization of existing natural resources to secure sustainable food production, including a fair use of agricultural land. To reach the 2030 targets, growers will need to change agronomic practices, including soil management, and minimize the use of chemical inputs, the consequences of which on soil microbial communities and plant nutrition are currently unknown.

IGATech Contest 2020: #scRNAseq Winner Project Presentation

Pleased to present the winning proposal “Understanding tumor and microenvironmental heterogeneity in primary and secondary cancers by single-cell RNA-seq” sent by the 31 y/o post-doctoral research fellow Elena Campaner from the University of Trieste.

#LabNote: A new solution for low input miRNA-seq

Deep sequencing of entire population of expressed miRNAs in a given sample simultaneously queries thousands of miRNA sequences with extraordinary sensitivity and ability to detect novel ones. In general, the approach is used to give insights in how post-transcriptional regulation contribute to phenotype and for the discovery and development of novel biomarkers for diagnostic testing. In addition, given its extreme sensitivity, miRNA-seq is suitable for detection of both RNA and DNA viruses, as well as viroids that can be missed using targeted detection methods.

Metabarcoding sequencing: moving from MiSeq to NovaSeq

DNA metabarcoding, i.e. targeted sequencing of taxonomically informative genetic markers, is an efficient method for the assessment and monitoring of biological diversity. Microbiome research is rapidly advancing boosted by sequencing of 16S rRNA gene and ITS region, while the noninvasively surveying plant and animal species richness from different ecosystems is nowadays routinely achieved through the sequencing of plastid or mitochondrial loci such as rbcL, matK and COI or cox1.

Amplicon-Seq for SARS-CoV-2 detection: tips for improved yields

Since studies related to COVID-19 are attracting great scientific interest, we recently focused our activities in recovery of viral sequences from swab samples by two methods: amplicon-Seq and RNA-Seq (using Trio RNA-Seq library preparation kit by Tecan Genomics as reported in our previous post).

Ultra-low RNA-seq for SARS-CoV-2 detection from nasopharyngeal swabs

In the last few months, we have been involved in several COVID-19 related activities and one of our main goals was to provide an effective way to retrieve viral sequences from swab samples. For this purpose we adopted mainly two methods: amplicon-Seq (based on the ARTIC protocol, for which we will discuss our results in another post) and RNA-Seq.  

Exome-Seq: #Quality #Genetics

Proud to announce that we are keeping our quality standards high by qualifying again above the mean in the external quality assessment of NextGen DNA Sequencing by the European Molecular Genetics Quality Network (EMQN).

Applying RNA-seq to COVID19 clinical samples

Sequencing of the SARS-Cov2 genomes using standard RNA-Seq strategies has been so far mainly achieved using viral culture or BALF, providing adequate viral copies as input template. However, for large-scale surveys of genome mutations, their spread, along with the ability to assess potential co-infections, the analysis of common swab samples with an unbiased RNA-Seq approach is an ideal solution, potentially, for any respiratory infection. 

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