Methods to do bulk sequencing of 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.

NGI offers several types of transcriptome sequencing approaches. Are you interested in analysing protein coding or non-coding RNAs, or small RNAs such as miRNAs? Get in touch with us to discuss the best approach for your project!

Please consult the flowchart for an overview of the applications that might best suit your project. You can also read more about each application further down in the applications section.

For projects focused on transcriptome annotation, please refer to our de novo page.

All new projects should first be discussed with us prior to placing an order through our online order portal. Please contact us here.

Standard short-read RNA-seq
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.
Illumina TruSeq Stranded mRNA

RNA sequencing of mRNAs selected through poly-A enrichment.

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.

Illumina Stranded total RNA Prep (Ribo-Zero Plus)

Total RNA sequencing based on reduced rRNA content and other type of highly abundant RNAs in both prokaryotic and eukaryotic samples.

Ion Torrent sequencing

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

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

miRNA libraries from very low input total RNA samples & degraded total RNA.

TaKaRa SMARTer pico RNA kit

The Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit is specifically designed for very low input total RNA samples. It also works with degraded total RNA.

PacBio Iso-Seq Analysis

With long and accurate HiFi reads, you can characterize the full diversity of the transcriptome

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.