Additional file 1: Fig. S1. Size distribution of surface RNAs analyzed in Surface-seq. Fig. S2. Size distribution of the Surface-seq constructed sequencing libraries. Fig. S3. TTD microscopy of EL4 cells. Fig. S4. Images of healthy donor PBMCs from imaging flow cytometry. Fig. S5. tSNE plots of isFISH sorted single cells. Fig. S6. Summary of Surface-FISHseq datasets. Table S1. Summary of Surface-seq libraries. Table S2. Summary of Surface-FISHseq libraries. Table S3. Probe sequences for Surface-FISH.