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Cell Profiling

National facility

The Cell Profiling facility enables researchers to access the resources and expertise from the Human Protein Atlas and the primary aim is to do full service immunofluorescence projects at moderate to high-throughput level. Based on the resource of more than 25,000 antibodies and a panel of >20 different human cell lines, this facility has a unique position to investigate subcellular spatial proteomics for human and rodent biology.

As you would only pay for the amount of antibody you use, the price per antibody is about 10 % of the vendor price, which allows you to stain for many more protein targets at a reasonable price.

In 2018 the Facility entered an Early Access program for the CODEX platform, as one of ten labs world wide.  The CODEX technology enables highly multiplex imaging (>30 protein markers) in fresh frozen (FF) and paraffin embedded (FFPE) tissue sections with spatial information at single cell level. The CODEX platform has now been integrated as a service in the facility and we are now accepting proposals for projects using the CODEX platform. You can read more about the CODEX platform here:

Contact us at to discuss how can your project benefit from this unique resource!


Open Call for project support in EPIC-XS infrastructures
The European Proteomics Infrastructure Consortium providing access (EPIC-XS) consists of a unified network of experienced access providers and research groups who share a common goal; to facilitate the development and sustainability of proteomics exploration to all life science researchers within the European Union. The Cell profiling Facility at SciLifeLab and other EPIC-XS connected facilities are now accepting new project proposals. Visit to submit proposals or contact directly for more information. DEADLINE FOR NEXT ROUND OF SUBMISSIONS CLOSES ON JUNE 30, 2020.


We perform everything from project design, sample preparation and imaging to give you as good results as possible. We share infrastructure and resources with the Human Protein Atlas and this include a proteome wide library of antibodies that can be used in tailor made projects to answer specific biological questions. You are also welcome to use our microscopes for imaging after an introduction with one of the staff scientists.

Proposed projects are assessed and prioritized according to the following model

Initial screen of project by facility:

1. Technical feasibility (yes/no)
2. Capacity requested for the project (classification: small/medium/large)

Project prioritization is based on:

1. Scientific potential
2. Supporting preliminary data
3. Supports facility development (competence and techniques)
4. Significance of facility specific technique for project

5. Feasibility of time lines


  • High-throughput profiling of protein targets in single cells using multiplexed immunofluorescence
  • Comparison of protein expression and localization in different cell states
  • Phenotypic screens
  • Immune cell distribution in tissue samples/tissue profiling of cellular phenotypes
  • Antibody validation and testing for further screens

Here are a few examples of previous projects:

  1. Explore the effect of a small molecule/substance on a particular organelle, family of proteins or proteins within a defined pathway.
  2. Screen for proteins co-localizing with a defined marker in different cellular conditions like autophagy, serum starvation or hypoxia.
  3. Confirm data from mass spectrometry experiments, such as translocation of proteins
  4. Evaluation of immune cell infiltration in muscle biopsies from diabetic patients before and after physical exercise
  5. Validate knock-out cell lines and antibodies by evaluation of fluorescence signal reduction and quantitative image analysis



  • Antibodies. 25,000 ICC validated antibodies from the Human Protein Atlas project.
  • Confocal microscope. 3 LEICA SP5 up-right confocal microscopes, 1 inverted SP8 confocal microscope, 1 DMI8 inverted screening fluorescence microscope
  • Liquid handling. Two TECAN FREEDOM EVO 150 pipetting robots. One TECAN Fluent 480.
  • CODEX platform, enabling highly multiplex imaging (>15) at single cell level in tissue sections


  • Validation of translocating proteins at subcellular level in T cells upon activation via the T-cell receptor. Confocal microscopy was applied to confirm novel translocalizing proteins observed from data of bulk populations by mass spectrometry. Front. Immunol., 26 November 2019 |
  • A screen of >100 nucleolar proteins in a model for ALS (amylotropic lateral sclerosis) to evaluate general morphology and function of nucleoli in normal and diseased ALS state. The hundred nucleolar protein targets were also used to confirm the effect of a small molecule identified in a previous screen, against the accumulation of toxic peptides in the nucleoli. Cell Chemical Biology (doi:10.1016/j.chembiol.2018.10.020).
  • A four-stage isogenic human cell model for malignant transformation was characterized with RNA-seq to identify differentially expressed genes. Subsequent functional analysis of the target proteins in the cell model was done at a single cell level using antibodies and confocal microscopy. We could in this manner characterize the molecular mechanism behind malignant transformation in this model and validate potential novel biomarkers of clinical interest. Danielsson et al, PNAS (Apr 2013).
  • A panel of 27 monoclonal antibodies were validated in different cell lines to evaluate their functionality as organelle markers for immunofluorescence applications. The antibodies validated by the Cell profiling Facility are now part of the Atlas Antibodies product portfolio.!/products/panel/organelle-markers