Protocol for purifying and sequencing cell subpopulations based on RNA FISH signal in planaria

Isolation and characterization of rare cell types in non-model organisms present a challenge. Here, we provide a protocol to purify specific cells from planaria for downstream RNA sequencing. We employ a one-step dissociation and fixation method that avoids RNA-degrading formaldehyde. We label cells using RNA fluorescence in situ hybridization (RNA FISH) and flow sort to enrich sequencing reads from cells of interest for deeper biological insight. For complete details on the use and execution of this protocol, please refer to Mann et al.