GSM8783784: WT_CnC10_GFPneg_HC_rep2; Mus musculus; ATAC-seq
To perform ATAC-seq, we FAN-sorted neuronal nuclei from viral déjà vu mice at different time points after intravenous wtLCMV challenge. Each biological replicate represents 50000  neuronal nuclei Neuronal nuclei were spun down at 500 g for 20 min at 4 °C. Nuclei were isolated in 50 μl of lysing solution composed of 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630. The nuclear pellet was resuspended into 50 μl of tagmentation buffer containing the Tn5 transposase (Illumina) and incubated at 37 °C for 30 min. The tagmented DNA was purified using MiniElute PCR Purification Kit (Qiagen). Libraries were preamplified for 5 cycles using indexed primer from Nextera kit (Illumina) and NEBNext High Fidelity PCR master mix (New England Biolabs). Preamplified libraries served as input to determine the number of remaining cycles needed for the second round of PCR amplification. ﻿Libraries were cleaned by Ampure Beads (Agencourt) at a 1.5× ratio.