2 min read project

See-N-Seq: Image-guided Single-Cell RNA Sequencing

Journal
Communications Biology, 5(1), 768 — 2022

Summary

See-N-Seq is a method for sequencing only the cells you visually target under the microscope.

Instead of randomly capturing cells, See-N-Seq uses a micropatterned hydrogel with controlled porosity in standard microwell plates. By locally increasing porosity around a chosen cell, the method allows:

  • selective lysis of the target cell
  • mRNA capture from that cell only
  • direct linkage between image-based phenotype and single-cell transcriptome

Why It Matters

Most single-cell RNA-seq platforms cannot choose cells based on what they are doing — only where they randomly end up in a droplet or well.

See-N-Seq enables:

  • sequencing cells forming an immune synapse
  • tracking specific interacting cell pairs
  • focusing on visually rare or dynamic events

My Role

As the first author, I led the development and validation of the See-N-Seq method from early concept to publication.

  • Concept & system design
    • Helped define the overall architecture of See-N-Seq: using a porous + non-porous hydrogel combination in standard imaging microwell plates to enable selective lysis of a single target cell without physically moving it.
    • Worked on translating the high-level idea (“sequence only the cell you see under the microscope”) into a concrete, step-by-step experimental workflow.
  • Hydrogel patterning & experimental workflow
    • Designed and optimized the hydrogel encapsulation process so that cells remain fixed in position between imaging and laser micropatterning steps.
    • Developed and refined the laser micropatterning protocol that embeds non-target cells in non-porous hydrogel while leaving the target cell accessible for lysis and RNA extraction.
    • Tuned parameters such as exposure, laser scan patterns, and gel composition to balance selectivity, RNA yield, and compatibility with standard 384-well plates.
  • Assay development & validation experiments
    • Designed and performed experiments to show that See-N-Seq can target single cells and cell–cell conjugates forming an immunological synapse, and still recover high-quality RNA for sequencing.
    • Helped establish controls comparing See-N-Seq to conventional single-cell RNA-seq workflows (e.g., RNA quality, gene counts, and reproducibility).
  • Data analysis & interpretation
    • Contributed to data processing and analysis linking imaging-derived phenotypes (e.g., T-cell / APC synapse formation and timing) to single-cell transcriptomic states.
    • Participated in interpreting results such as the time-dependent bifurcation of helper T-cell lineages after synapsing.
  • Writing, figures, and communication
    • Prepared a large portion of the figures explaining the workflow, hydrogel design, and example applications.
    • Drafted and revised major sections of the manuscript, and coordinated feedback across co-authors to shape the final narrative.
  • Intellectual property & translation
    • Listed as an inventor on IP related to See-N-Seq and related hydrogel-based cell capture imaging reagents, supporting potential translation of the method beyond a single paper.

Vaughn Lee