RNAseq via ribodepletion
Learn more
RNA-seq will be applied to quantify the gene expression patterns of human tissue, blood, plasma or cells as well as identify gene fusions. This will allow for the identification of cell types present in a sample, characterization and quantification of cell type specific expression patterns and study phenotypic differences between tissue/cell types, different treatment conditions and healthy vs disease.
Sample types
Blood > RNA
PAXgene Blood RNA tube
10 ml (2,5 ml blood)
Ice pack
Blood > cfRNA/exoRNA
Streck RNA Complete BCT
10 ml
Room temperature
Cells of various tissue origins > RNA
Microtube* with cells on lysis buffer
> 5 million cells
Dry ice
FFPE block of various tissues > RNA
Paraffin block (in cassette)
Representative block ; Tumor load preferentially >10% ; To be processed by our pathology department (microtome section needed)
Room temperature
FFPE section of various tissues > RNA
Microtube*
Min. 1x 10 µm section (up to 2 mm³ tissue) ; Tumor load preferentially >10%
Room temperature
Plasma > cfRNA/exoRNA
DNA LoBind 5 ml tube
> 2ml
Dry ice
RNA from various tissues > RNA
Microtube*
See test details/specifications
Ice (max. 20 min) or dry ice
RNA from various tissues > RNA
Microtube* or 96 well plate
See test details/specifications
Ice (max. 20 min) or dry ice
Tissue of various origins > RNA
Cryovial containing stabilizer (eg. RNAlater) or tissue homogenized on lysis buffer
Application/tissue specific (contact us)
Dry ice
Extra requirements
Minimum DV200
RNA tube & plate - Diagnostic
Minimum: 30 %
Below a DV200 of 30% we experience lower yields or total library prep failure. Please provide us with a new sample if this requirement is not met.
Absorbance ratio A260/A230 - Minimum
RNA tube & plate - Diagnostic
Minimum: 1,5
Lower values are indicative for indicative for EDTA, carbohydrate, chaotropic salts (and also protein) contamination
Absorbance ratio A260/A280 - Minimum
RNA tube & plate - Diagnostic
Minimum: 1,5
Lower values are indicative for indicative for protein, phenol or other aromatic compound contamination
Elution buffer : nuclease free water
RNA tube & plate - Diagnostic
:
Please use nuclease free water as an elution buffer for your RNA samples. Other buffers (e.g. containing EDTA) may inadvertently affect our assays
Minimum RNA quantity
RNA tube & plate - Diagnostic
Minimum: 200 ng
Below 40 ng of input, success rate is very low without adjusting PCR cycles. Please provide us with as much as material as possible (200 ng preferred).
Deliverables
Below, you can find the type of data files that can be retrieved for this test.
If you require more information or need a more custom output, please consult our Bioinformatics page.
Count file
Text file containing the reads per transcript (HTseq output)
RUO
Fusion report
HTML based report, containing results from Fusioncatcher, Arriba and STAR fusion
RUO
MultiQC report
HTML document visualizing all relevant quality metrics for your batch of samples
Diagnostic / RUO
Raw data - bam file
Binary data file containing the aligned reads
RUO (on request)
Raw data - fastq file
Data file containing the raw (unaligned) reads
RUO (on request)
Documents & certificates
Validated
Plan experiment
For Diagnostics
This test is also performed as a diagnostic assay. In this case, please contact your General Practitioner, Pathologist, haematologist or Clinical Geneticist (Centre for Medical Genetics or haematology department of choice) to get the diagnosis started.
For Research
This test can also be applied in context of research. For this, please get approval from your local ethical committee and/or make proper arrangements with your Biobank.
Please follow the steps below to start up an experiment with us.
Get in touch (ONLY FOR NEW PROJECTS)
Explain your project, so we can assist you to find the best solution.
Expect questions like :
What type of sample would you like to analyze?
Which elution buffer did you use?
What are the expected concentrations of your samples?
How many samples would you like to process?
How fast do you need the results (TAT) and/or do we need to expedite?
If you deviate from our sample types, are there test samples available?
Are our standard deliverables ok?
...
1
Request quotation
Once you know which experiment you want to set up, fill out the 'Quote request' form, with the essential details of your project :
Coordinates of the person to whom to address the quotation
Which type of test you'd like to set up
Do you require a specific deliverable?
Do we need to expedite (comes at extra cost)?
...
2
Submit your samples
Once you agree with our terms (quote / TAT / terms & conditions) :
Fill out our sample submission form
Send it via email : contact us
Print out the form and include it with your samples
Send your samples to us
Label your tubes/plates correctly : see details here
Adhere to the corresponding transport conditions listed under Sample types
Indicate if we can discard your samples after completion of project
3
Your experiment starts
Now it is up to us... We will start your experiment as soon as possible.
When expedited, the turn-around-time (TAT) is 2,5 weeks
For standard requests the turn-around-time (TAT) is 2 months
The standard TAT is generally overestimated, but this extended timeframe allows us to : combine similar requests of multiple scientists and to repeat the experiment in case of issues.
Please refrain from contacting us in case the pre-agreed TAT didn't expire yet.
