In Situ Sequencing (ISS), the next generation of sequencing technologies
CARTANA’s technology is based on In Situ Sequencing (ISS), the next generation of sequencing technologies. ISS is a new type of nucleic acid analysis performed directly on the tissue section, preserving the spatial information.
The technology uses gene specific barcoded padlock probes that detect and amplify the targeted genes of interest in situ, directly on the brain section using the rolling-circle-amplification. Next-generation-sequencing chemistry is applied directly on the tissue sections to sequence the amplified barcode sequences. Our analysis software package decodes the barcode sequences, thereby identifying and quantifying the genes.
The result is a map of gene expression data of all analyzed genes and their abundance with sub-cellular resolution on top of the natural morphology of the tissue section.
Xiaoyan Qian et al., “Probabilistic cell typing enables fine mapping of closely related cell types in situ“ (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)
Xiaoyan Qian et al., “A spatial atlas of inhibitory cell types in mouse hippocampus“ (2018,
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