Fig. 6
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Fig. 6
RNA Tomography Allows Construction of a Spatially Resolved Transcriptome-wide Atlas of Gene Expression in 3D
(A) Mathematical approach for 3D image reconstruction based on 1D projections. The expression pattern of a hypothetical gene is shown as a green square in the left panel. The middle and right panel show reconstructed expression patterns after sequential optimization steps in blue. Measured 1D tomo-seq traces are depicted as green lines, projections of computationally reconstructed image on x and y axis are shown as blue lines to the left of and under the panels. The steps shown here were iterated 100 times for optimal image reconstruction.
(B–D) Normalized expression patterns of selected genes (blue) after 3D image reconstruction. The shape of the embryos is shown in black and white. (B) Left: expression of lft1 at 15 somites stage in a plane perpendicular to LR axis through the middle of the embryo. Middle and right: lft1 expression in the two planes indicated by red lines in the left panel. (C) Projection images (summed over LR axis) for lft1, mespab, and myl7 expression patterns at 15 somites stage. (D) Left: projection along animal-vegetal axis for gsc and ntla at shield stage. Middle: expression in a plane perpendicular to animal-vegetal axis at the level of the margin. Right: expression in a plane perpendicular to LR axis through the middle of the embryo.
See also Figure S6 and Data S2.
Reprinted from Cell, 159, Junker, J.P., Noël, E.S., Guryev, V., Peterson, K.A., Shah, G., Huisken, J., McMahon, A.P., Berezikov, E., Bakkers, J., van Oudenaarden, A., Genome-wide RNA Tomography in the Zebrafish Embryo, 662-75, Copyright (2014) with permission from Elsevier. Full text @ Cell