NGI during Covid-19 outbreak

NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.

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Transcriptomics

Methods to sequence protein coding, non-coding or small RNA, with short or long reads. Select an application to learn more about its advantages and sample requirements. We also offer different options for low input samples or degraded RNA within each application.

Gene expression
Investigate transcription levels and isoforms, e.g. for studies of differential expression.
Small RNA
Assess the abundance and identity of different small-RNA such as miRNA, directly from total RNA.
Full-length transcripts
Full-length sequencing of RNA transcripts can be used to investigate splicing isoforms and fusion-gene transcripts, as well as annotation of de novo genomes.
Spatial transcriptomics
Quantification of transcription within the spatial context of intact tissue.
Illumina TruSeq Stranded mRNA

RNA sequencing of mRNAs selected through poly-A enrichment.

Illumina TruSeq Stranded total RNA (RiboZero)

RNA sequencing of all RNA in a sample after depletion of rRNA or another type of highly abundant RNA.

Illumina TruSeq Stranded RNA without selection or depletion

RNA sequencing of either all RNAs in a sample, or of a RNA sample depleted of for example rRNA by the user.

10X Genomics Visium

We offer spatial transcriptomics through the 10X Genomics Visium method. The method combines histology with unbiased transcriptomics in a spatial context.

Illumina TruSeq Small RNA

Generation of sequencing libraries from dicer cleaved miRNA.

Ion Torrent sequencing

Ion Torrent semiconductor sequencing technology is as simple as it is fast.

Loop Genomics sequencing

Loop genomics can provide both transcript counting and phasing for full length mRNA using short-reads on Illumina sequencers

Nanopore cDNA sequencing

Nanopore cDNA sequencing is able to sequence entire transcripts in one go, ideal for detecting isoforms and fusions events.

Nanopore Direct RNA sequencing

Nanopore direct RNA sequencing is able to sequence entire transcripts from native RNA, opening up opportunities to detect RNA modifications.

PacBio SMRT sequencing

PacBio SMRT sequencing generates reads tens of kilobases in length enabling high quality genome assembly, structural variant analysis, amplicon resequencing, full-length transcript isoform sequencing, full-length 16S rRNA sequencing and amplification free epigenetic characterization.

QIAseq miRNA low input

Generation of miRNA libraries from very low input total RNA samples and degraded total RNA.

TaKaRa SMARTer pico RNA kit

The Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit is specifically designed for very low input total RNA samples. It also works with degraded total RNA.

PacBio secondary analysis

Analysis applications provided by NGI using PacBio’s open-source SMRT Analysis software suite.

PromethION secondary analysis

Additional compute intensive nanopore raw data processing services provided by NGI

Illumina QC analysis

Basic quality-control monitoring of Illumina FastQ sequence data.

RNA-fusion analysis

Runs with illumina RNA-Seq data. Aligns to the reference genome, gives QC metrics, predicted gene fusions and finishes with graphically visualised reports.

RNA-seq analysis

Runs with illumina total RNA-sequencing data. Aligns to the reference genome, gives QC metrics and finishes with gene count matrices.

Small-RNA analysis

Runs with illumina small RNA-sequencing data. Aligns to the reference genome, gives QC metrics and finishes with gene count matrices.