Gene-expression profiling

Sequencing of all protein-coding transcripts

Sensitive indicator of changes in biological processes

Gene-expression profiling is the most popular method since it provides a total overview of the expression levels in your sample. All protein-coding (poly-A containing) transcripts are consistently and accurately represented. It provides an affordable approach to examine differential gene-expression analysis between groups of samples, such as various treatments, time-points, or disease versus control samples.

Our ISO-accredited service includes all novel features: Unique Molecular Identifiers (UMIs), identification of antisense transcripts, and can handle a broad range of input RNA, starting from 5 ng. It is applicable for FFPE-material or other (partly) degraded and challenging samples (see below).

For whole blood analysis, we offer globin reduction that removes the globin transcripts originating from erythrocytes, so you reduce the sequencing capacity that is required per sample with 30 to 40%. The removal of ribosomal RNA is not necessary, since these transcripts do not contain a poly-A tail. For custom transcript removal or targeted RNA seq-approaches, contact our scientific support team.

Our experienced bioinformaticians generate quality assured data-sets or deliver publication-ready results through our validated pipelines. For more demanding projects our experts work closely with you to provide a fully custom analysis.

Working collaboratively at each stage of your project:

Product specifications 1 01 Product page Gene expression profiling
  • mRNA measurement based on poly-A selection
  • Globin reduction for whole blood samples is optional
Sample specifications 2 01 Product page Gene expression profiling
  • Optimal total RNA input: 100 ng / sample
  • Ideally deliver ≥250 ng RNA to allow for QC and normalization
  • Minimally validated RNA input: 10 ng
  • For RNA quality of RIN / RQN ≥7
Deliverables 3 01 Product page Gene expression profiling
  • Sequencing of poly-A containing transcripts
  • Quality score Q30 of ≥80% for PE 150 reads
  • TAT: 3 weeks
Sequencing 4 01 Product page Gene expression profiling
  • Sequencing on NovaSeq 6000 PE150 or NextSeq 500 SR75
  • Gene-expression analysis: 20 million reads

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This amount is sufficient for performing a statistically sound transcriptome analysis. It is a  more accurate and complete alternative for micro-array sequencing. Contact customer support if you require another amount of reads per sample.

  • Structural variant analysis

To determine structural variation such as isoforms, splice variants and gene-fusions we advise a sequencing depth of 50 – 100 million reads per sample. You will receive a full transcriptome analysis, as well as a reliable overview of SNPs and structural rearrangements.

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Data quality 5 01 Product page Gene expression profiling

The specifications of the data-set that you will recieve are listed in your personal quotation. Generally, the sequencing quality score is Q30≥80% for PE 150 reads (Illumina’s official guarantee ≥75%). Our average score of 2018 was Q30≥90%.

Data analysis 6 01 Product page Gene expression profiling
  • Gene-expression analysis (raw data)
  • Count table
  • PCA plot, heatmap, pathway analysis

We have summarized key information about our gene-expression profiling service into a product specification sheet, which you can download here.

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Discuss you project with Andre

We have over 15 years of experience in the transcriptomics field. Talk with us about best practices and how we can help your research.

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Andre Wijfjes

Manager Customer Support

+31 71 568 1036

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