FINGEEC FAQ

Please check below some of the most frequently asked questions regarding our services.

Cell line generation services

  1. Does FinGEEC perform a functional validation of the knockout phenotype in edited cells?
    • No, customers are responsible to check the functional validity of the knockouts.
  2. How do I validate my cell line for a knockout phenotype?
    • Phenotypic consequences of the targeted mutation by CRISPR should always be validated (usually loss of protein expression). The fastest ways to validate knockouts are western blotting, flow cytometry or RT-qPCR (sometimes RNA expression is lost as well). It is always recommended to monitor the known downstream effect of target knockout if possible.
  3. How do I design my CRISPR knockout project?
    • We provide free consultation to customers who have no prior knowledge of CRISPR/Cas9 editing. Contact information is (here).
  4. What is the success rate of any genome editing project?
    • CRISPR/Cas9 editing has its limitations and success of projects at FinGEEC or anywhere depends on multiple factors. Most of the variables relate to how different cell lines behave during any given genome editing project. Editing conditions are very often unique to each cell line and gene target. 
  5. Do I absolutely need gRNA validations before starting editing in cells?
    • No, but It is strongly recommended to validate whether you have a functional gRNA in actual cellular conditions. While the accuracy of the Sanger gRNA library and online portals or vendors in gRNA designing is in principle very good, the functionality can not be estimated without testing it in your desired target cells.
  6. Can we knockout a gene although it is an essential gene for cell survival and/or proliferation/growth?
    • No, if the gene is absolutely essential for cell survival and growth, FinGEEC will not be able to knockout the gene (and make clones). To find out, if your putative target gene is "common essential", go to DepMap. From there it possible to seen how your intended target cell line(s) would handle the loss-of-function of your putative target gene. Limitation here is that the database has only cancer cell lines.
  7. I need a knockout of a gene and I can't predict its viability effect in my target cell line.
    • One way to check if cells can tolerate knockout, is to perform a transient (siRNA/shRNA/CRISPR) transfection in your own lab to see effect of gene knockdown on cell growth and health. If cells tolerate knockdown, there is a good chance to acquire knockout cell clones for your target gene.

 

Digital slide scanning service

 

  1. How do I know if my slides are suitable for scanning?
    • The scanner takes standard 25x75mm microscope slides and allows variation in slide thickness between 0.9-1.2mm. If you are not sure whether your slides meet these requirements, we have a tool for measuring the slides.
    • All slides to be scanned must be mounted with a solidifying mounting media and the coverslips must not protrude over the edges of the microscope slide (see more instructions for prepping the slides below).
    • For each sample type we can perform a test scanning free of charge.
  2. Do I need to know how to operate the equipment and how can I make a reservation?
    • Slide scanning is operated as a service, so we will take care of the scanner runs and provide you with the images. However, we would be happy to do test scannings with you as well as demonstrate how the equipment works if you are not familiar with this technique.
    • For reservations: please send email to fingeec-support@helsinki.fi describing the type of samples you have and how many slides you'd like to have scanned. We will suggest a schedule for your scanning project depending on the current situation.
  3. What kind of image files the scanner produces and how can I view them?
    • The image data for each slide consists of a folder and a .mrxs-file with the same name. When copying the images, please make sure you copy both the folder and the .mrxs-file in order to open the image in the viewing software.
    • You can view the slides using a 3DHISTECH software (Pannoramic Viewer or CaseViewer, both can be freely downloaded from their website). The softwares are available for Windows only. You can also view your images using Biomedicum Imaging Unit imaging workstations.
    • Using the viewing softwares it is possible to export selected areas in tiff or jpeg format.
  4. How do I receive the image files?
    • Please note that the image files can be large (up to several GBs / slide with bright field). Images are saved on the scanner computer R: drive immediately following scanning. The network connections of the scanner computer are restricted and for the brightfield images it is recommended you copy the files straight from the computer to your own portable drive. As the fluorescent images are usually smaller, it is possible also to distribute them using Funet FileSender server.
    • You can copy the images while the scanner is running. Please do not remove the files from R: drive, just copy them to your own disk.
  5. Can I have the image files named according to my samples?
    • If the scanner has generated names to your image files they are named with a running number from 1M01 to 1M25 for the first magazine capable of taking 25 slides, then 2M01-2M25 and so forth.
    • For the automated bright field runs, it is possible to import sample names to the scanner and the image files will be named accordingly. Please ask for more details on how to provide FinGEEC with the name list.
    • It is also possible to change the image file names later on utilizing standard file management. However, please make sure you rename both the folder and the .mrxs-file.
    • The scanner is equipped with a bar code reader if your slides are labeled with 1D or 2D barcodes.
  6. How can I see the frosted end of the scanned slide?
    • It is always possible to see the frosted end of the slide with the sample details. In Pannoramic Viewer when viewing one slide, click the button with "i" icon on top ot the window. Choosing "slide information" will open a window where with an image of the frosted end and details of the scanning (objective, scanning time, image file size, layers, for fluorescence exposure times).
  7. What if I receive an image that is not focused well, parts of the sample is missing or is otherwise of poor quality?
    • Please contact FinGEEC for rescanning the slide. For difficult samples, it is possible to use more focusing points or apply extended focus option.