Fixed brain tissue was cryopreserved in 30% sucrose at 4°C overnight and embedded in water-soluble glycols and resins (Tissue-Tek O.C.T. Compound, 25608-930, Sakura Finetek Europe B.V., AJ Alphen aan den Rijn, The Netherlands) for the production of coronal sections (14-μm thick) using a cryostat (Leica Microsystems, Wetzlar, Germany). For RC2, BLBP, Slit1 and Pax2 immunohistochemistry, brain sections were blocked with 3% BSA, 10% normal goat serum (NGS) in 0.1% PBS-Triton X-100. Radial glial markers: RC2 (mouse, 1:5; Developmental Studies Hybridoma Bank), BLBP (rabbit, 1:500, ab32423; Abcam, Cambridge, UK), Slit1 (rabbit, 1:500, PAB11326; AbNova, Taipei, Taiwan) and embryonic development marker Pax2 (rabbit, 1:100, 901001; BioLegend, San Diego, CA, USA) were diluted in blocking solution at 4°C overnight. For CS-56 and H2B immunohistochemistry, brain sections were blocked with 3% NGS in 0.2% PBS-Triton X-100. CSPG markers: CS-56 (mouse, 1:500, C8035; Sigma-Aldrich Corp., St. Louis, MO, USA) and H2B (mouse, 1:500, 370710-IEC; Amsbio, Madrid, Spain) were also diluted in blocking solution and incubated at 4°C overnight. Where the primary antibody was raised in mouse, a mouse on mouse Ig blocking solution (BMK-2202; Vector Laboratories, Burlingame, CA, USA) was applied to avoid nonspecific staining. For each set of immunostaining, a no primary antibody control was included to ensure staining was specific (
Supplementary Figs. S2,
S3). For the CSPG, crushed optic nerve samples were also analyzed to visualize the injury site (
Supplementary Fig. S4). For GFAP, NG2, Iba1, and Olig2 immunohistochemistry, brain sections were blocked with 2% BSA, 5% NGS in 0.5% PBS-Triton X-100. GFAP (chicken, 1:1000, ab4674; Abcam), NG2 (rabbit, 1:200, AB5320; MilliporeSigma, Burlington, MA, USA), Iba1 (guinea pig, 1:500, #234004/6; Synaptic Systems, Göttingen, Germany) and Olig2 (rabbit, 1:500, AB9610, MilliporeSigma) were diluted in blocking solution at 4°C overnight. Slides were washed three times for 10 minutes with PBS. Anti-rabbit Alexa Fluor-555 (1:500, A-21429; Invitrogen, Carlsbad, CA, USA), anti-mouse Alexa Fluor-555 (1:500, A21424; Invitrogen), anti-rabbit Alexa Fluor-488 (1:500, A11034; Invitrogen), anti-chicken Alexa Fluor-488 (1:500, A11039; Invitrogen), anti-rabbit Alexa Fluor-647 (1:500, A32733; Invitrogen), anti-mouse Alexa Fluor-488 (1:500, A11029; Invitrogen), anti-guinea pig Alexa Fluor-555 (1:500, A21435; Invitrogen) and anti-guinea pig Alexa Fluor-488 (1:500, A11073; Invitrogen) were used as secondary antibody with a 2-hour incubation period at room temperature, followed by counterstaining with DAPI. Slides were washed three times for 10 minutes with PBS and mounted with glass coverslips and reagent (FluorSave, 345789; MilliporeSigma).