Microglia ATAC-Seq Library Preparation

ATAC-Seq libraries were constructed as described before^{35 (link)}. Fifty thousand isolated microglia were lysed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl₂, 0.1% NP-40). Following lysis, nuclei were tagmented using the Nextera DNA library prep kit (Illumina) for 30 minutes. Then DNA was purified and amplified for 12 cycles. The libraries were sequenced with a 50bp paired end read. After removing the adapter and low-quality sequences, the data were aligned to the mm10 genome with Bowtie2. Peaks were called on aligned sequences using MACS2 with -p 0.01 --nomodel --shift -37 --extsize 73 -B --SPMR --keep-dup all options. Peaks were then evaluated with less than 0.01 irreversible differential rates. Differentially accessible regions were identified using Diffbind-EdgeR with FDR<0.05^{56 (link)}. Deeptools and HOMER were employed for further analyses, including motif enrichment analysis with the indicated options.