Scientific Documents

In this section, we have collected a number of Scientific White Papers where we describe the researcher’s application of our technology and  Scientific Publications related to In Situ Sequencing technology.  We will continuously add more titles to our current collection.

White Papers

“Spatio-Temporal Structure of Cell Fate Decisions in Murine Neural Crest ” by Soldatov R, Kaucka M. and Kastriti M.E ( Science, 2019).

In this study of the cell fate decision progress of neural crest cells, In Situ Sequencing by Cartana proved to be a crucial complement to the standard methods of single cell sequencing. For the first time, the molecular logic of cell fate decision involved in these rapidly changing cells was revealed- by the dimensions of time and space.

Read the White Paper here.


Xiaoyan Qian et al., “Probabilistic cell typing enables fine mapping of closely related cell types in situ (2019, Nature methods)

Hernandez, et al.: “Application Note: Mapping brain cell types with CARTANA in situ sequencing on the Nikon Ti2-E microscope” (2019, Nature methods) 

Ke, et al.: “In situ sequencing for RNA analysis in preserved tissue and cells” (2013, Nature methods) 

Grundberg, et al: “In situ mutation detection and visualization of intratumor heterogeneity for cancer research and diagnostics(2013, Oncotarget)

Mignardi, et al: “Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ” (2015, Nucleic Acids Research)

Ke, et al: “Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences” (2016, Human Mutation)

Kühnemund, et al: “Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy” (2017, Nature Communications)

Mathot, et al: Somatic ephrin receptor mutations are associated with metastasis in primary colorectal cancer” (2017, American Association for Cancer Research)

Dou, et al: “Analysis of IAV Replication and CO-infection Dynamics by a Versatile RNA Viral Genome Labelling Method” (2017, Cell Reports)

Xiaoyan Qian et al., “A spatial atlas of inhibitory cell types in mouse hippocampus (2018, 

Zaghlool, et al: “Expression profiling and in situ screening of circular RNAs in human tissues” (2018, Scientific Reports)

Tiklová, et al: “Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development” (2019, Nature Communications)

Carow, et al: “Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma” (2019, Nature Communications)

Soldatov, et al: “Spatiotemporal structure of cell fate decisions in murine neural crest” (2019, Science)

Chen, et al: “Spatial and temporal transcriptomics reveal microglia-astroglia crosstalk in the amyloid-β plaque cell niche of Alzheimer’s disease” (2019, bioRxiv)

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