SFO grants 2020

We are happy to congratulate the following seven researchers to SFO infrastruture grants 2020!

Qiaolin Deng
Qiaolin Deng, Associate professor & PI, at Dept.Physiology and Pharmacology, is the main scientific advisor together with Assoc. Prof. Eduardo Villablanca.

Qiaolin Deng

The single-cell technology core at the Center for Molecular Medicine (CMM) is equipped with 10x Genomics and Tecan Fluent 780 automated workstation as well as several essential accessory equipment (i.e. Agilent bioanalyzer 2100, Formulatrix Mantis, BluePippin etc) to perform fundamental single-cell/low-input high-throughput assays.

Massive single-cell profiling by 10x Genomics across multiple molecular layers is now routinely used by many researchers to address cellular heterogeneity, gene expression and regulation within tissue or cell population. To counteract the relatively low sensitivity of tag-based methods, our core has also set up a fully automated sequencing library preparation pipeline with liquid handing robots (Tecan Fluent 780 and Formulatrix Mantis) to perform Smart-seq2 full-length RNA-sequencing with sorted single cells in microtiter plate format (96- or 384-well).

The core has recently established Smart-seq3, the latest full-length single-cell RNA-seq for sensitive and in-depth gene expression analyses with allelic and isoform. Tecan fluent 780 is an advanced automated workstation 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. This automation pipeline is configurable and can be adapted to run other plate-based protocols including ATAC-seq (Transposase Accessible Chromatin with high-throughput sequencing), single-cell bisulfite sequencing and single-cell WGA (whole-genome amplification). In addition, low-input small RNA-sequencing protocol will be soon setup

Anna Falk, Researcher at Department of Neuroscience

Anna Falk

The iPS Core facility will develop a human brain organoid platform to be widely available to KI scientists as a fee for service and with a first come first served policy. The iPS Core will set-up human brain organoids for the following studies by the customer:

 

  • Disease modelling and comparison studies (including neuronal functionality) of organoids derived from iPS cells of healthy or diseased individuals. 
  • Develop human organoids that will act as hosts and “in-vivo-like” brains for transplanting cells to study either cancer and tumour development or cell replacement therapy.
  • Screening set-up in 96 well format assaying neural networks and functionality.
Massimiliano Gaetani, Head of the Chemical Proteomics facility at Department of Medical Biochemistry and Biophysics.

Massimiliano Gaetani

The Chemical Proteomics facility of KI (MBB), national facility at SciLifeLab and BioMS (Biological Mass Spectrometry) infrastructures, supports research projects using LC-MS-based approaches. In particular among them, it provides advanced proteome-wide methods, early adopted and developed in house, identifying and quantifying proteins key of early and functional responses to cell treatments and phenotype changes, including target identification and elucidation of action mechanisms.

The Chemical Proteomics facility

The facility is well equipped for BSL2 cell culture, LC-MS-based proteomics and bioinformatic data analysis. The support provides complete pipelines including culturing cells in situ, LC-MS-based proteomics and data analysis. This model is transferred to recently integrated skills and equipment dedicated to stem cells and regenerative medicine.

Photo of Anna Pasetto, Managing director of the pre-GMP facility in ANA Futura
Anna Pasetto, Managing Director of the Pre-GMP facility in ANA Futura

Anna Pasetto

The pre-GMP facility, located in the ANA Futura building at KI Campus Flemingsberg, is a recent addition to Vecura. The pre-GMP facility offers laboratory space and offices, as well as technical support, for ATMP-related projects that need process development before actual GMP manufacturing. One of the key features of the pre-GMP facility is the possibility for users to access state of the art advance equipment to test and optimize their manufacturing processes.

The pre-GMP facility together with Vecura can offer full support to the potential users from the starting of the process optimization until the GMP manufacturing and clinical trial.

The HTGE/KGE Group

Bernhard Schmierer

High Throughput Genome Engineering/Karolinska Genome Engineering (HTGE/KGE) is both a National SciLifeLab facility and a Karolinska core facility, and is the foremost competence center for high-throughput CRISPR application in the Nordics. We are based in Biomedicum in Solna and provide a wide range of services using CRISPR/Cas technology to researchers from all over Sweden. Our core services are pooled, lentiviral CRISPR screens from several hundred targets to genome-wide; small pooled screens followed by single cell RNASeq readout; the creation of precision-edited cell lines and reagent design for mouse transgenesis. We are continuously developing and updating our expertise and service portfolio. For more information, please see our webpages below or drop us an email!

Erik Sundström
Erik Sundström, Researcher at Department of Neurobiology, Care Sciences and Society Photo: Stefan Zimmerman

Erik Sundström

The Developmental Tissue Bank is a service for KI researchers who needs human embryonic-fetal tissue for their research projects. We retrieve the tissue from routine abortions, through a collaboration with local gynecology clinics. Tissue is transferred to the core facility in Huddinge or Solna, we define the post-conception age, identify the tissue parts and perform dissection. The tissue is processed according to the requests from our clients, and stored or delivered immediately. From autumn 2020 we will be able to prepare cells for single cell RNA-sequencing or FACS, and deliver to the respective core facility for an extra fee. Tissue for clinical use is prepared in Vecura, the Karolinska cell therapy facility.

The tissue collected can be delivered immediately to the user or stored in the tissue bank, which is a part of the Stockholm regional biobank (Stockholms Medicinska Biobank – SMB). Tissue delivered without prior treatment is usually kept in commercial hibernation medium, but when necessary it can be kept in other cell media, RNAlater or other solutions depending on what is requested by the user. Tissue can also be fixed or snap-frozen in 2-methylbutane-dry ice. We usually freeze tissue in cryo molds with OCT or in RNAlater. Other procedures can also be arranged.

When tissue is intended for clinical use it is prepared in the cell and gene therapy facility Vecura (Huddinge). Each user receiving tissue on a regular basis pays a fee per 6 months. Since we do not have control over the number of patients recruited, we charge half the standard fee for periods when we deliver tissue from less than 8 cases per 6 months. For users requesting fewer samples, we apply a fee per sample.

Developmental Tissue Bank Facility
The Developmental Tissue Bank

To get access to tissue from the Developmental Tissue Bank, you send an e-mail to devtissuebank@nvs.ki.se describing what you are interested in, and a one-page description of the project. We first arrange a meeting to discuss what you need and what we can retrieve and collect at various developmental stages. For some tissues and organs we may first have to do tissue sectioning and histological analysis to determine what is possible to dissect at what stages. Sectioning and staining can either be done by the user, or by the core facility for an extra fee.

When human prenatal material is used for research, ethical permits as well as permits from the National board of health and welfare (“Socialstyrelsen”) and SMB are required. We will assist in writing these application, and guide all users through the required procedures.

Michael Vanlandewijck 
Michael Vanlandewijck, Assistant professor, Department of Medicine Huddinge

Michael Vanlandewijck 

In spring 2017, the Single Cell Core (ScCore) was created at the Integrated Cardio Metabolic Centre (ICMC) in response to an increased demand from ICMC scientists for single cell sequencing solutions. We mostly perform 384 well plate based sequencing using Smart-seq2 chemistry in a highly efficient and miniaturized format. In light of the increased demand for single cell transcriptomics at KI, the facility is converting from a private in-house facility to a full open access, non-profit, KI core facility operating with subsidized user-fees. The main goal of the Single cell core facility is to provide expertise and experimental support on single cell technologies for researchers at KI, starting with advice on experimental setup and selection of available technology leading all the way up to delivery of clustered single cell data in a format that can be explored by researchers without the need for specialized bioinformatics expertise.

Junior Grant 2020

  1. Eduardo Villablanca
  2. Francois Lallemend
  3. Fredrik Lanner
  4. Makoto Sahara
  5. Maria Genander
  6. Ulrika Marklund
  7. Volker Lauschke