Related Experiment Video
Updated: Aug 4, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis
Published on: December 14, 2017
Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications
Anastasia Magoulopoulou1, Sergio Marco Salas1, Katarína Tiklová1
1Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; email: anastasia.magoulopoulou@scilifelab.se, sergiomarco.salas@scilifelab.se, katarina.tiklova@scilifelab.se, erik.samuelsson@scilifelab.se, markus.hilscher@scilifelab.se, mats.nilsson@scilifelab.se.
Abstract:
Elucidating spatiotemporal changes in gene expression has been an essential goal in studies of health, development, and disease. In the emerging field of spatially resolved transcriptomics, gene expression profiles are acquired with the tissue architecture maintained, sometimes at cellular resolution. This has allowed for the development of spatial cell atlases, studies of cell-cell interactions, and in situ cell typing. In this review, we focus on padlock probe-based in situ sequencing, which is a targeted spatially resolved transcriptomic method. We summarize recent methodological and computational tool developments and discuss key applications. We also discuss compatibility with other methods and integration with multiomic platforms for future applications.
Related Concept Videos
Sanger Sequencing
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Labeling DNA Probes
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
In-situ Hybridization
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...

