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Single-particle tracking of filaments was performed manually in Volocity.
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Phosphohistone H3+ cells were counted either from a z-max projection of all focal planes, manually using the Image "cell counter" plug-in, or from a 3D reconstructed image in Volocity using the object recognition software.
Distance measurements were performed in Volocity by locating the centres of each of the pair of centroids manually and measuring the distance along a straight line between the two centroids.
All images were deconvolved using the iterative or the fast restoration algorithms in Volocity.
The 3D reconstruction in Fig. 1C was made in Volocity (Improvision).
Images from each embryo were cropped in Volocity (Improvision) to exclude the neural tube.
Images captured using the spinning disk were processed and analyzed in Volocity 4.20.
Confocal files were imported in Volocity and analysed the same way.
mRNAs in each cell were subsequently identified according to their size and SD intensity as in Santangelo et al [9] and combined with the RNA granules using the "exclude-non touching objects" tool in Volocity.
Quantification was done in Volocity.
Videos were reassembled in Volocity for deconvolution.
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