Data for 3D reconstruction of the corticospinal tract in the wild-type and Semaphorin 6A knockout adult brain

The corticospinal tract (CST) has a complex and long trajectory throughout the brain. Semaphorin 6A (Sema6A), a member of the semaphorin family, is one of the important regulators of CST axon guidance. Previous studies have shown that Sema6A knockout (KO) mice have CST defects at the midbrain–hindbrain boundary and medulla [1]. However, the route of the aberrant fibers remained unknown. Therefore here, to track the trajectory of the abnormal fibers, 3D images of the CST in adult mice were reconstructed from serial brain sections stained with anti-PKCγ antibody. Sema6A mutant brains showed CST defects that were more complex and variable than previously thought. In addition, 3D analysis helped us to identify a few new patterns of abnormal fibers. For more information about the data, please refer to an original research article, which has been recently published by Brain Research, “Remarkable complexity and variability of corticospinal tract defects in adult Semaphorin 6A knockout mice” [2].


a b s t r a c t
The corticospinal tract (CST) has a complex and long trajectory throughout the brain. Semaphorin 6A (Sema6A), a member of the semaphorin family, is one of the important regulators of CST axon guidance. Previous studies have shown that Sema6A knockout (KO) mice have CST defects at the midbrainehindbrain boundary and medulla [1]. However, the route of the aberrant fibers remained unknown. Therefore here, to track the trajectory of the abnormal fibers, 3D images of the CST in adult mice were reconstructed from serial brain sections stained with anti-PKCg antibody. Sema6A mutant brains showed CST defects that were more complex and variable than previously thought. In addition, 3D analysis helped us to identify a few new patterns of abnormal fibers. For more information about the data, please refer to an original research article, which has been recently published by Brain Research, "Remarkable complexity and variability of corticospinal tract defects in adult Semaphorin 6A knockout mice" [2].

Data
3D images of the CST trajectories throughout the adult mouse brains were reconstructed from serial sections stained with anti-PKCg antibody. Each movie shows 360-degrees horizontal and vertical rotation of the 3D images of the CST. Images from one wild-type mouse (movies 1e3) and three Sema6A KO mice (movies 4e6, 7e9, 10e12) are shown.
The image of the wild-type mouse (shown in pale green) is inserted into the movies of Sema6A KO mice (pale blue). The characteristics of the datasets (dataset name, image attributes, file type, file size, and description of dataset) are summarized in Table 1.

Animals
The Sema6A KO mice were described previously [1,3]. All animal experiments were approved and performed according to the guidelines of the Animal Care and Use Committees of the University of Tsukuba and the National Institute of Neuroscience, National Center of Neurology and Psychiatry.

Immunohistochemistry
Cryostat sections (50 mm) of paraformaldehyde-fixed adult mouse brains were dehydrated, treated with 3% H 2 O 2 in 80% methanol, 20% dimethyl sulfoxide (DMSO) for 30 min, rehydrated, and incubated Specifications Value of the data These data describe the use of 3D reconstruction of the CST from serial antibody-stained sections to visualize the nerve trajectory throughout the mouse brain. 3D reconstruction reveals the complex and variable CST defects in the Sema6A KO mice, which otherwise is difficult to intuitively notice using brain section analysis. These data provide detailed information on the abnormalities of the neural circuits in the adult Sema6A KO mouse, which is valuable to understand the neurologic and psychologic deficits in the mutant mice [3] and human diseases. Movie showing a reconstructed 3D image of the CST of the wild-type mouse brain. The area from the cerebral peduncle to the dorsal funiculus is shown. This movie corresponds to the 3D reconstruction in Fig. 4A-A 00 in Ref. [2]. The lateral ( Figure Fig. 6A-A 00 in Ref. [2]. The lateral ( Figure 6A), ventral ( Figure 6A 0 ), and frontoventral ( Figure 6A 00 ) views are seen as the frames at 24, 41, and 36 seconds from the beginning of the movie, respectively. "Movie 1" of the wild-type mouse brain (pale green, inset) is shown as a reference.  Fig. 6B-B 00 in Ref. [2]. The lateral ( Figure 6B), frontal ( Figure 6B 0 ), and frontoventral ( Figure 6B 00 ) views are seen as the frames at 24, 0, and 37 seconds from the beginning of the movie, respectively. "Movie 2" of the wild-type mouse brain (pale green, inset) is shown as a reference.
(continued on next page) with anti-PKCg antibody (1:200; Frontier Institute, Hokkaido, Japan) at 4 C twice overnight. After  Fig. 6C-C 00 in Ref. [2]. The lateral ( Figure 6C), frontal ( Figure 6C 0 ), and ventral ( Figure 6C 00 ) views are seen as the frames at 25, 0, and 40 seconds from the beginning of the movie, respectively. "Movie 3" of the wild-type mouse brain (pale green, inset) is shown as a reference.  Fig. 7A-A 00 in Ref. [2]. The lateral ( Figure 7A), ventral ( Figure 7A 0 ), and frontoventral ( Figure 7A 00 ) views are seen as the frames at 24, 40, and 37 seconds from the beginning of the movie, respectively. "Movie 1" of the wild-type mouse brain (pale green, inset) is shown as a reference.  Fig. 7B-B 00 in Ref. [2]. The lateral ( Figure 7B), frontal ( Figure 7B 0 ), and frontoventral ( Figure 7B 00 ) views are seen as the frames at 24, 0, and 37 seconds from the beginning of the movie, respectively. "Movie 2" of the wild-type mouse brain (pale green, inset) is shown as a reference.  Fig. 7C-C 00 in Ref. [2]. The lateral ( Figure 7C), frontal ( Figure 7C 0 ), and ventral ( Figure 7C 00 ) views are seen as the frames at 25, 0, and 40 seconds from the beginning of the movie, respectively. "Movie 3" of the wild-type mouse brain (pale green, inset) is shown as a reference.