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Spatial Transcriptomics at the Single-Cell Level

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NanoString on August 3, 2022

Is spatial transcriptomics single-cell resolution?

Yes. Recent advances in the field of spatial transcriptomics have made it possible to visualize RNA transcripts at the resolution of a single-cell and, in some cases, subcellular resolution.

Image-based spatial transcriptomics methods provide single-cell resolution using in situ hybridization techniques. Single-cell imagers use sequential cycles of probe hybridization and imaging and offer the potential to combine the benefits of scRNA-seq analysis with added spatial resolution at single-cell or even subcellular resolution.

What is single-cell analysis used for?

Single-cell analysis can provide data on cellular phenotypes by studying the effects of genomic alterations, gene expression, and environmental influences at the level of a single cell.

Data obtained through single-cell analysis provides an excellent opportunity to dissect the composition of complex tissue and gene-regulatory networks that drive cellular identity and function in diverse tissues and conditions. Single-cell analysis can help uncover cellular heterogeneity and identify rare cell populations, distinct cell-lineage trajectories, and mechanisms involved in complex cellular processes of an individual cell. The core components of single-cell analysis are (1) technologies for single-cell isolation, barcoding, and sequencing to measure different types of molecules from the same cells, and (2) integrative analysis of the molecules measured at the single-cell level to identify cell types and their functions related to pathophysiological processes based on the molecular signatures.

Which technique is used for single-cell isolation?

Techniques for single-cell isolation are primarily based on either the physical properties of the cell, such as size, density, and electric changes or on cellular biological characteristics such as surface protein expression.

Some methods based on physical properties include Manual cell picking and Laser Capture Microdissection (LCM). Manual cell picking is a simple technique that consists of an inverted microscope combined with motorized micro-pipettes that can move to pick out a single cell under direct microscopic visualization, thus enabling unbiased isolation. The major advantage of this technique is that it can be applied to isolating live culture cells or embryo cells. Laser Capture Microdissection (LCM), on the other hand, is an advanced technology for isolating cells of interest by visualizing under the microscope and cutting away unwanted cells to give a histologically pure enriched cell population. The advantage of LCM is that it conserves spatial information of mRNA expression within the morphology of a tissue. 

Flow cytometry techniques that are based upon properties of protein expression, such as Fluorescence-Activated Cell Sorting (FACS) and Magnetic-Activated Cell Sorting (MACS), are also commonly used. FACS uses the specific light scattering fluorescent characteristics of each cell which have been labeled with an antibody marker coupled with a fluorescent dye, whereas MACS uses magnetic particles that bind cells through an antibody interaction with surface markers of the targeted cell that are magnetically isolated from the sample mix.  

Microfluidics is another powerful technology to sort cells that provide precise fluid control, low sample consumption, device miniaturization, and easy handling of nanoliters-volumes. Microfluidic cell sorters can be classified as either active or passive. Active systems generally use external forces such as electric, magnetic, and optical to displace cells for sorting, whereas passive systems use inertial forces, filters, and adhesion mechanisms to purify the cell population.

For Research Use Only. Not for use in diagnostic procedures.

Post by NanoString