Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation

Probe-Seq is a method that allows transcriptional profiling of specific cell types from heterogeneous tissue by labeling RNA. Briefly, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated based on RNA abundance of defined markers. We applied Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas as well as the Drosophila gut. We also showed that Probe-Seq is compatible with frozen nuclei and that multiplexed Probe-Seq enables iterative isolation of multiple cell types from the same tissue sample. Provided that unique markers are available, this simple, novel method could potentially enable bulk RNA sequencing of any cell type from any organism. Overall, RNA sequencing was peformed on mouse retina whole cell, mouse retina nuclei, Drosophila gut, and developing chick retina. For the mouse retina whole cell experiment, 3 populations, Vsx2-, Grik1-, and Grik1+ populations were isolated for RNA sequencing, with 2 biological replicates each. For the mouse retina nuclei experiment, 2 populations, Grik1+ and Grik1-, were isolated for RNA sequencing, with 3 biological replicates each. For the Drosophila gut, 2 populations, esg+ and esg-, were isolated for RNA sequencing, with 3 biological replicates each. For the chick retina, 2 populations, FGF8+ and FGF8-, were isolated for RNA sequencing, with 3 biological replicates each.