Fig. 1

Sequencing and validation of maxRNA from a cell line. a, b The workflow of the two variations of Surface-seq. c A Venn diagram of the noncoding RNAs identified by the 5 Surface-seq experiments, indexed by A1, A2, A3 (based on Surface-seq variation A), and B1, B2 (based on Surface-seq variation B). d Read coverages from the 5 Surface-seq libraries on the MALAT1 gene, indexed by A1, A2, A3, B1, and B2. Red arrowheads: locations of Surface-FISH probes. e A hypothetical model of the relative positions of Surface-FISH probes (red arrowheads) on a membrane-bound Malat1 RNA fragment. f Box plots of the numbers of Surface-FISH signal foci per cell (y-axis) for Malat1, Neat1, and two controls (mut-Malat1, mut-Neat1) (columns). N: number of cells examined. g, h Malat1 Surface-FISH (g) and DIC image of the same cell (h). The green dashed lines outline the rim of the cell. i, j Control probeset mut-Malat1 Surface-FISH (i) and DIC images of the same cell (j). k, l Malat1 Surface-FISH (k) and transmission-through-dye (TTD) image of the same cell (l). Arrows: Malat1 Surface-FISH signals. The TTD image was produced by a membrane-permeable dye used in conjunction with a membrane-impermeable quencher, indicating a cell with an intact cell membrane. Scale bar = 5 μm. Probe signals were compared against corresponding controls. ***p value < 0.0001