Next Generation Sequencing - Powered by Innovation & Expertise

INVIEW Transcriptome Discover

Discover and quantify transcripts and splicing variants.

Strand-specific RNA sequencing offers gene expression data in relation to strand orientation. This approach is ideal for genome annotation, studying antisense or overlapping transcripts, and discovering novel transcripts.

In addition to RNA sequencing, we offer RNA isolation services and a variety of library preparation protocols tailored to your specific project needs. These include poly(A) selection methods for eukaryotic organisms when only mRNA data is needed. rRNA depletion for studying special RNA species such as lncRNAs or poor-quality RNA (e.g. FFPE) for a variety of organisms (e.g. human, mouse, rat and plants) is also available. For blood RNA, we provide globin depletion.

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Applications

Elucidate cellular function through transcript quantification
Analyse specific genomic elements and their biological significance
Characterise differences in RNA splicing like alternative splicing
Identify antisense transcripts
Determine transcribed strand of non-coding RNAs
Mark boundaries of closely situated or overlapping genes

Highlights

Strand-Specific RNA-Seq
Short turnaround times starting from 15 working days
Unique Dual Indexing (UDI) ensures high-quality data.
Guaranteed data output, starting from 5M read pair packages
Highly sophisticated bioinformatics services & analysis reports
Data transfer via secure FTP

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Product Specifications & Ordering

Our standard RNA-Seq analysis pipeline provides a comprehensive approach to understanding gene expression, beginning with quality assessment of sequencing data. We align reads to a reference genome, quantify transcripts, and normalize gene counts, followed by principal component analysis (PCA) to visualize sample relationships and identify expression patterns. Finally, we identify differentially expressed genes through significance testing, generating detailed reports and visualizations—including heatmaps, volcano plots, and various QC metrics—to empower researchers with meaningful biological insights.

Optional RNA-Seq analysis packages:

Alternative splicing (AS) analysis: This analysis is available for designs with replicates in a case vs. control setup and provides a detailed view of the alternative splicing events that occur in the samples.
Gene Fusion Analysis: This analysis is available for single sample onwards and provides a detailed view of the gene fusions that occur in the samples.
Variant detection and its effect on protein alteration: This analysis is available for single sample onwards and provides a detailed view of the variants that occur in the samples and their effect on protein function.
Gene Set Enrichment Analysis (GSEA): This advanced bioinformatics analysis service utilizes Gene Set Enrichment Analysis (GSEA) to identify biological pathways and gene sets that are significantly enriched in differentially expressed genes. This analysis provides a deeper understanding of the biological processes and pathways that are affected by the changes in gene expression.

For optional RNA isolation service, please refer to our “Sample preparation and shipping guide for Extraction”. 

We do not accept samples with higher biosafety level than S2. GMOs are only accepted with S1 level.

Specifications

Entry QC of RNA quality and RNA quantity
Illumina-compatible stranded RNA-Seq library preparation using Unique Dual Indexing
Technology: Illumina NovaSeq 6000 or NovaSeq Xplus
Run type: paired-end
Read length: 2 x 150 bp
Guaranteed data output for predefined or flexible read packages (multiples of 5 Mio read pairs), depending on your needs we recommend 20-30 million read pairs for large genomes (e.g., human, mouse) and 15-20 million read pairs for medium genomes (e.g. yeast).

Starting material and RNA selection methods

Sample Type: total RNA (DNA-free)
Purity (OD260/280): 1.8-2.2
Recommended RIN: ≥8.0
Resuspension Buffer: Nuclease-free water or Tris-HCL buffer (pH 7.5 to pH 8.0)
Format: barcode labelled 1.5 ml safe-lock tubes; or for > 48 samples in Eppendorf twin.tec PCR Plate 96, full-skirted, leave position G12 & H12 empty 
Shipment Method: Dry ice, contact us about our recommendation for RNA Stabilization Tubes to ship RNA samples at ambient temperature.

RNA selection method	target RNA	Minimum amount	Minimum volume	Concentration
none	Total RNA	20 ng	10 µl	2 - 20 ng/µl
Poly(A)selection	mRNA (eukaryotic)	150 ng	25 µl	6 - 200 ng/µl
rRNA depletion	mRNA + lncRNA	375 ng	10 µl	37.5 - 200 ng/µl
globin + rRNA depletion	mRNA + lncRNA (blood)	500 ng	10 µl	50 - 400 ng/µl

RNA selection methods:

Pre-Sequencing Service	This service includes	You get data for	Comment
RNA-seq without PolyA or Depletion	cDNA library generation of all present RNAs	Total RNA	You receive data for the total RNA including high abundant RNAs like rRNA (~90 % of total RNA) and specific mRNAs
Poly-A-selection	Bead-based poly-A-selection of your samples (mRNA enrichment)	Only mRNA	This service targets polyA-tails (mRNA) in a total RNA sample. Therefore, only polyA containing fragments will be targeted and sequenced. mRNAs usually make up only 1 to 2 % of the total RNA. If your samples have poor quality (e.g. FFPE material), the mRNA may be degraded. This would result in mRNA fragments without polyA tails which then could not be targeted. If you expect poor quality you might get better data for your research question with selecting rRNA depletion
rRNA depletion	Bead-based rRNA depletion of your total RNA samples (HMR/Bacteria/Plant)	Total RNA minus rRNA	This service targets ribosomal RNA and will remove it from the total RNA. Usually, rRNA make up ~90 % of total RNA. All remaining RNAs, including mRNA, tRNA lncRNAs, etc. will be prepped and sequenced
globin depletion	Bead-based depletion of globin mRNA of your samples	Total RNA minus globin mRNA	This service targets globin mRNA and will remove it from the total RNA. The remaining RNAs will be prepped and sequenced. This service can be combined with: rRNA depletion or PolyA enrichment, a minimum of 48 samples per project is required

Library types

Standard eukaryotic library - mRNA is poly-(A) enriched and fragmented. cDNA synthesis is performed using random hexamer priming.
Standard prokaryotic library - rRNA is removed by ribo depletion. cDNA synthesis is performed with random hexamer primers.
Library with FFPE RNA - RNA isolation from Formalin Fixed Paraffin Embedded (FFPE) samples with optimised ribodepletion for reliable gene expression analysis and SNP detection.
Strand-specific library