Project workflow

Project workflow


1. Project meeting

For users without prior experience in single-cell sequencing or spatial transcriptomics analyses we recommend a project meeting where we can discuss about your project and decide the most suitable analysis method for it. Contact us for more information.

2. Service Request

Register and sign in to online project management system iLab and submit a Service Request. Follow the general instructions for iLab use or contact us to get help with iLab and Service Request submission.

3. Reservation for sample delivery

Single-cell sequencing services: Available analysis slots can be viewed in iLab Booking calendars. Make a reservation by contacting the SCA unit via your submitted iLab Service Request.

Spatial transcriptomics services: Agree on the sample delivery by contacting the SCA unit via your submitted iLab Service Request.

4. Updates on sample delivery (Single-cell sequencing services only)

On the day of the experiment, send us updates on your sample delivery schedule. Both email and mobile phone messages work.

5. Sample library preparation and next generation sequencing

Preparation of Illumina short read sequencing ready sample libraries and Next Generation Sequencing in FIMM SCA and Genomics Sequencing units.

5. Data processing and analysis

Generation of raw sequence files and pipeline analysis performed in FIMM SCA unit.

6. Data release

You will receive a data release email via iLab that contains information about the performed analysis as well as data location and access.

7. Acknowledge us

To help us secure our support from University of Helsinki (HiLIFE) and Biocenter Finland in the future, we ask all users of FIMM SCA and Genomics Sequencing unit services to acknowledge us in publications containing data produced in the units.


Sample requirements

The condition and viability of the cells strongly affects the quality of the single-cell sequencing data.

Optimization of the tissue dissociation and processing may be needed prior single-cell sequencing analysis.

Contact us to get information about the recommended cell processing protocols.