The calculated clonality rates represent the likelihood that any individual cluster of labeled cells is indeed clonal, based on the results of this simulation analysis.
The main cluster of labeled neurons was arranged in a stem-like column ventral to RA (robust nucleus of the arcopallium), while a distinct 'stripe' of labeled neurons was observed 300 400 µm anterior to the main cluster.
This revealed a discrete cluster of motor neurons in the thoracic spinal cord, which correspond to the motor neurons innervating the abdominal muscles, and a cluster of labeled motor neurons in the facial nucleus of the brainstem, corresponding to those motor neurons innervating the cranial muscles (Fig. 3).
They all comprised a single large cell corresponding to the neuroblast as well as an associated cluster of labeled cells corresponding to the secondary neurons, and the secondary axon tracts formed by the secondary neurons had an appropriate, wildtype-like projection pattern in all cases (supplementary material Fig. S1).
Individual gold labels cannot be distinguished at this magnification, but clusters of labels are visible as bright spots in the image.
One more element is required to fully reproduce every aspect of the clustered labeling patterns seen in cortex: a rule is needed that produces discrete clusters of label far from a large injection site.
In contrast, following 2-AAF treatment the proportion of labeled cells dropped and only rare large clusters of labeled hepatocytes were detected.
Importantly, clustering of labeled RGCs was observed in retinas that received 4HT after E11, a time when there are already many hundreds of retinal progenitors and lateral migration of cells within a single retinal clone is severely restricted [10].
The auditory shelf directly ventral to the medial ∼2/3rds of HVC that shows auditory-induced expression (Fig. 6A, 3rd and 4th row) did not show any clusters of labeled neurons in the hopping deaf animals (Fig. 6C; Fig. S4Aa).
Small injections would result in clusters of labeled somata but diffuse anterograde labeling of boutons.
