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Cell Observatory Core

The Cell Observatory core at CMM strives to provide both full service and advanced equipment access on the self-service base for spatial and single cell library preparation and full training for spatial, single cells and bulk library preparations.

​for single cell transcriptomics, we currently run Smart-seq3 plate-based full-length protocol, and all available protocols for droplet based single cells capture with 10X Genomics. For spatial transcriptomics we run Visium (10x genomics) and for spatial proteínica we run ChipCytometry from Canopy.

Other available equipments are:

  • ​Tecan Fluent Robotic System (an automated solution for genomic workflows) – this instrument will move out from CMM soon. CMM members will have access to the instrument at a different location. Contact peri.noori@ki.se for more information.
  • Mantis Nano Dispenser
  • Chromium controller and Chromium iX
  • Agilent bioanalyzer
  • Pippin Gel Extraction Prep System (DNA Size Selection for PCR fragments and NGS, 100bp – 1.5kb).
  • PCR machines 384 w, 96 w
  • Microscopes for spatial transcriptomic


Tecan Fluent Robotic System (an automated solution for genomic workflows)

Tecan fluent 780 at single cell core facility is an advanced automated workstation which can help you with fast dispensing, transferring or removing low volumes of liquids (0.5 μl to 125 μl in the 384-well format, and 0.5 μl to 500 μl in the 96-well format) with high accuracy. It equips with either 8-channel FCA arm or 384/96-multi channel arm which allows various workflows. A separate robotic gripper arm is used for moving plates on the worktable and acquire plates on the deck. Currently, Smart-seq3 protocol is in-built to perform bead purification and liquid transfer. You are welcome to design and optimize your own assays on it! For more technical and practical detail, please visit https://lifesciences.tecan.com/fluent-laboratory-automation-workstation and contact Peri Noori (peri.noori@ki.se).

Pippin Gel Extraction Prep System (DNA Size Selection for PCR fragments and NGS, 100bp – 1.5kb).

We also welcome users to set up their own automation protocols using our equipments.

We can consult with library pooling for sequencing.

Location: The facility is located at CMM L8:01 room 052.

Responsible person:

Contact Peri Noori, for more information and introduction.

E-mail: peri.noori@ki.se

Scientific advisor:

Eduardo Villablanca

E-mail: eduardo.villablanca@ki.se

About CMM

The Center for Molecular Medicine (CMM) is a foundation instituted by the Stockholm County Council (Region Stockholm). CMM is at the heart of a close partnership with the Karolinska University Hospital and Karolinska Institutet, fueling advancements in biomedical and clinical research.


Center for Molecular Medicine Foundation, org. nr. 815201-3689

Karolinska University Hospital L8:05

Visionsgatan 18

171 76 Stockholm, Sweden


Karolinska institutet
Karolinska universitetssjukhuset