For confirming the interaction between neuroLNC and TDP-43, we used a RIP protocol. For this purpose, the cortices of P2 rats were homogenized by a micropestle in low-sucrose buffer [0.32 M sucrose, 5 mM CaCl2, 5 mM Mg(Ac)2, 0.1 mM EDTA, 50 mM Hepes (pH 8), 1 mM DTT, and 0.1% Triton X-100] on ice. The lysate was cross-linked by 1% formaldehyde and neutralized with 1.25 M glycine. In the following steps, the lysate was washed two times with 1 ml of cold Nelson-Jameson buffer (150 mM NaCl, 20 mM EDTA, 50 mM tris, 0.5% NP-40, and 1% Triton-X-100) and incubated in lysis buffer [100 mM tris-HCl (pH 8), 20 mM EDTA, and 2% SDS] for 10 min at 4°C. The lysate was precleared with Dynabeads protein A (Invitrogen) and then incubated with rabbit anti-rat TDP-43 antibody (Proteintech, no. 10782-2-AP) or Syntaxin 1A (SYnaptic SYstem, no. 110 302) as a negative control overnight and with beads for additional 1.5 hours at 4°C. After several washing steps, RNA was eluted from beads and purified by an miRNeasy Mini Kit (Qiagen). To achieve high-quality samples, RNAse inhibitor (SUPERase.In, Invitrogen) and protease inhibitors (phenylmethylsulfonyl fluoride and Roche cOmplete EDTA-free protease inhibitor cocktail) were added to all solutions. The purified RNA was either sequenced or reverse-transcribed for qRT-PCR analyses.

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