The right answers to frequently asked questions
Find the answers to all our products and services by clicking the links below.
What kind of samples can be processed with INVIEW CRISPR Check?
The starting material is amplicons prepared in your lab that span the mutation site. The amplicon generation protocol to apply depends on the product type (adaptor ligation or 2nd PCR workflow), instructions can be found in the tab "How to prepare your Amplicons" on the respective product webpage. Amplicon length requirements can be found in the tab "Specifications".
Why is the recommended amplicon size range rather narrow?
For INVIEW CRISPR Check, the wildtype amplicon size needs to be adapted to the length of InDels you want to be able to analyse and must allow merging of read pairs. Usually mutations introduced via the NHEJ pathway are in a range of 1-20 bp, but in order to not miss the larger ones, the wildtype amplicons must be in a rather narrow size range. Length requirements for two use cases and all product types are available in our sample preparation guide.
Can I use your service if we used another CRISPR system than SpCas9?
Yes you can. In that case please provide the cleavage offset of your system (number of nucleotides upstream of PAM sequence where double strand break is expected).
What do you recommend for the assay setup?
- Always include at least one unmodified (wildtype) sample as control
- Include replicates if you aim for a very accurate prediction of the editing efficiency. Replicates increase accuracy of predicted editing efficiency, but are not strictly necessary.
How should I choose between INVIEW CRISPR Check Adaptor Ligation and INVIEW CRISPR Check 2nd PCR?
Both product types are excellent solutions to analyse mutations introduced by CRISPR/Cas system (NHEJ pathway).
The products vary mainly in the sequencing library preparation (2-step protocol vs. adaptor ligation protocol) and thus in the way you are preparing amplicons for sequencing.
A selection guide is available at the CRISPR website (tab Overview) to help you find the best solutions for your individual preferences.
What deliverables does your analysis provide?
- Comprehensive report with results and methods sections
- Raw FASTQ files
- Quality clipped and assembled FASTQ files
- Mapped reads in BAM format
- Observed wildtype and alternate allele sequences including their quantification
- Raw data, preprocessing, mapping, and coverage metrics in CSV format
- Calculated Editing Efficiency per sample
Where do I get my results?
For INVIEW CRISPR Check 2nd PCR the result files can be downloaded from a secure FTP server (password will be provided), for INVIEW CRISPR Check Adaptor Ligation the results will be delivered via your Ecom account.
Where should I send my samples?
Eurofins Genomics Europe Sequencing GmbH
When choosing INVIEW CRISPR Check 2nd PCR, can we send samples that consist of several amplicons generated with different primer pairs?
Usually you would send per sample 1 amplicon generated with 1 primer pair.
In some cases you might require however less reads per amplicon as given in the Project Specification. In such cases the individual amplicon samples you send may also consist of several amplicons.
Please note, that in this case however we will not perform the clipping of primer sequences and deliver raw data only.