Supplementary Materials

Highly Multiplexed Subcellular RNA Sequencing in Situ

Je Hyuk Lee, Evan R. Daugharthy, Jonathan Scheiman, Reza Kalhor, Thomas C. Ferrante, Joyce L. Yang, Richard Terry, Sauveur S. F. Jeanty, Chao Li, Ryoji Amamoto, Derek T. Peters, Brian M. Turczyk, Adam H. Marblestone, Samuel A. Inverso, Amy Bernard, Prashant Mali, Xavier Rios, John Aach, George M. Church

Materials/Methods, Supporting Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Supplementary Text
  • Figs. S1 to S14
  • Tables S1 to S4
  • References

Images, Video, and Other Other Media

Movie S1
3D rendering of the whole-transcriptome amplicons in human iPS cells visualized using
scanning confocal microscopy. Regions of low RNA abundance are observed as
fluorescence-free region such as intercellular junctions and the nuclear membrane.
In certain phases of the iPS cell growth, RNA in the nucleolus becomes inaccessible
to our method, visible as a hollow dark center in the nucleus.
Movie S2
3D rendering of the whole-transcriptome amplicons and the early chromosome
condensation in human iPS cells visualized using confocal microscopy.
Movie S3
3D rendering of the whole-transcriptome amplicons in a nucleolus-like body visualized
using confocal microscopy. Typically, one nucleolus consists of ~100 cDNA
amplicons in iPS cells.
Movie S4
Time series of 30 sequencing cycles in primary fibroblasts.
Movie S5
Time series of 30 sequencing cycles in primary fibroblasts (zoomed).
Movie S6
3D rendering of the 30-base sequencing run in human primary fibroblasts. Time
(sequencing base) is represented on the z axis, allowing one to visualize each
sequence as a vertical string of sequences within the cell.

Revised 4 March 2014: The correct Fig. S1 has replaced Fig. 1 from the report.
The original version is still available here.