INVIEW Transcriptome Discover

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.

• 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).

• 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 methods: 

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• 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

• Illumina
• 150 bp paired-end reads
• 30 million read pairs guaranteed

All details about our bioinformatics pipeline can be found here >>

15 days for up to 192 samples
20 days for up to 400 samples