Gene expression profiling 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.
Gene Expression Profiling
Sequencing of all protein-coding transcripts
Why analyse gene expression?
How can I help you?
A sensitive indicator of changes in biological processes
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 10ng. All protein-coding (poly-A containing) transcripts are consistently and accurately represented.
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.
Service workflow
1. Initial meeting
When you consider using one of our services, our scientific team will help choosing the optimal project design. Each service can be customized by adding options. You will receive an overview of project budget and deliverables, so you can make an informed choice. Once you return your Purchase Order form, your project manager will contact you to discuss the next steps.
2. Sample delivery
Sample specifications for gene expression profiling are:
- Optimal total RNA input: 250ng-1000ng / sample
- Ideally deliver ≥250ng RNA to allow for QC and normalization
- Minimally validated RNA input: ≥10ng
- For RNA quality of RIN / RQN ≥7
3. Sample entry QC
After sample arrival, an entry QC is performed to determine if the sample quality is sufficient so we can guarantee the data outcome stated in your quotation. You will receive a report with sample QC results to inform you of our findings before proceeding further. Samples that fail QC can be replaced by spare samples delivered in the same shipment or sent at a later stage.
4. Library prep/QC and sequencing
Sequencing on Illumina NovaSeq 6000 PE150
- Gene expression analysis: 20 million reads
This amount is sufficient for performing a statistically sound gene expression analysis. Contact customer support if you require another amount of reads per sample.
5. Data QC
The raw data that is generated by the sequencer must be divided to obtain one data file per sample. This is called demultiplexing.
Your project manager checks the data quality by analyzing the quality metrics of the run. Final inspection of the data takes place and the dataset is transferred onto our portal. It is also possible to receive your data on hard disk.
6. Reporting
You receive your Project Report together with your data. It contains an overview of the experimental methods used, sample specifications, and a summary of all technical information for publication. Deliverables:
- TAT: 3-5 weeks
- Gene-expression analysis (raw data)
- Quality score Q30 of ≥80% for PE 150 reads
- Count table (optional)
- Differential gene expression analysis (optional)
- PCA plot, heatmap, pathway analysis (optional)
Data analysis
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.
Principle component analysis, gene ontology enrichment and hierarchical clustering are examples of our extensive data analysis options for gene expression profiling.
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.
Service specifications
We have summarized key information about our gene expression profiling service into a service specification sheet.
Let's get the conversation started for your next NGS project
Please either fill in this form or email us directly at info@genomescan.nl
and we will get in touch with you to discuss your requirements
