Chika Yokota

Imaging Session

Wednesday, September, 29th, 2021: 12:00pm – 1:30pm

Placing RNA in context and space – A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections

The in situ sequencing Facility unit (Head), Department of Biochemistry and Biophysics, Stockholm University

Science for Life Laboratory


Recent advances of image-based in situ transcriptomics quantification methods allow to visualize the exact location of genes expressed in a tissue. 

In this talk, I would like to bring to your attention a high throughput, multi-targeted gene expression profiling technique called in situ sequencing (ISS) that enables localization and quantification of a few hundred transcripts simultaneously with single cell resolution in a single tissue section per experiment. 

The technique has been developed by Prof. Mats Nilsson, who has pioneered in the field of generating gene expression (Ke, R., et al. 2013 Nature Methods 10, 857-860) and mutation profiling information in situ, and it has been successfully demonstrated for a wide range of applications such as mapping of molecularly defined cell types, RNA editing, intra tumor heterogeneity and immune-cell profiling across various tissue types. 

The unique features of ISS technology are; 1) targeted method using padlock probes 2) highly specific amplification providing robust detection also in tissues such as human brain and tumors with high auto fluorescence 3) multiplexing, up to a few hundred transcripts per sample 4) sensitivity is tunable 5) high throughput due to wide-field imaging 6) compatible with formalin fixed paraffin embedded (FFPE) tissues. 

I will also highlight the recent technological developments of the method and the integration of spatial multi omics data.


Chika Yokota studied Developmental and Molecular Biology, and earned her Ph.D. from the University of Tokyo, Japan, working with Prof. Makoto Asashima.

In 2001, she moved to the United States to expand her skills and gain further experience as a senior scientist. At the beginning of her career, her research interest mostly focused on understanding some of the molecular mechanisms regulating early inductive events in the developing embryo. In particular, she focused on studying the role of TGF-b and Wnt signaling in dorso-ventral axis formation. She screened for, and succeeded in isolating, novel regulators of both the TGF-b and Wnt pathways. Two projects that she pursued during these years (at Children’s Hospital in Cincinnati and Harvard Medical School in Boston) were published successfully.

In 2008, she joined the Ludwig Institute for Cancer Research in Stockholm as a research associate/senior scientist with some lab manager responsibilities.

In 2017, when the in situ sequencing (ISS) pilot facility was launched at Stockholm University/SciLifeLab, she joined the pilot facility as a pilot facility manager. During this period, she implemented an automated instrument for the barcode sequencing reaction, which improved sample throughput and consistency in the sample preparation. The robustness of the existing laboratory infrastructure was also assed in order to promote a service based performance. A number of projects representing different kinds of potential user cases had been run by her and resulted in publications. In 2019, the ISS facility was launched as a national facility at Stockholm University/SciLifeLab, providing services under the Spatial and Single Cell Biology platform. She has been working as a Head of Unit since then. The platform covers cutting-edge technologies for spatial profiling of transcripts, proteins, DNA and small molecules, as well as several approaches for single cell analysis.




Twitter: @MatsNilssonLab


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Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development