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10X Genomics: CARTANA

Next generation In Situ technology

Spatially decode up to hundreds of genes simultaneously, within morphologically intact tissue samples at single cell resolution.

In Situ analysis is an innovative method of nucleic acid analysis performed directly in situ on the tissue section, preserving spatial information.

In Situ technology allows researchers to analyze either fresh/fixed frozen or FFPE samples and rapidly create single-cell gene expression maps of up to hundreds of genes.  The technology ensures high performance (high specificity and high throughput) and reliable, reproducible data.

Library Preparation

The highly specific padlock probes will hybridize to the RNA corresponding to your genes of interest.

The closed circle is then copied locally by a DNA polymerase in a rolling circle amplification (RCA) reaction. This generates a spot of the detected RNA transcript that includes multiple copies of the in situ barcode sequence corresponding to the detected gene at the original position of the RNA target.

Imaging cycles & Decoding

Barcodes are decoded from target-specific spots generated during the library preparation.

  • Decoding starts with the hybridization of the 1st adapter probe pool to the spots and binding of the fluorescently labeled sequencing pool probes to the adapter probes.
  • After imaging, the signal is removed to perform the next cycle.


Once all cycles are analyzed, each spot provides a unique fluorescent barcode identifying the targeted RNA.


Tissue Map

Our In Situ technology results in a map of gene expression of selected genes while preserving tissue morphology.


In Situ analysis of 31 transcripts in fresh frozen human breast cancer samples using In Situ technology.