ChIP-Atlas: SRX8339976

Antigen

Cell type Class: Neural
Cell type: Visual Cortex
MeSH Description: Area of the OCCIPITAL LOBE concerned with the processing of visual information relayed via VISUAL PATHWAYS.

library_strategy: ATAC-seq
library_source: GENOMIC
library_selection: other
library_construction_protocol: INTACT-purified nuclei were resuspended in L1 buffer (50mM Hepes pH7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 0.25% Triton X-100, 0.5% NP40, 10% Glycerol, protease inhibitors, sodium butyrate), and centrifuged at 2000 rpm at 4°C. L1 buffer was removed, and INTACT-purified nuclei were incubated with Tn5 in TD buffer (Illumina) for 30 minutes at 37°C. To control for potential biases for Tn5 towards specific sequence compositions, we performed the above assay on naked genomic DNA isolated from cortices. Adapter-ligated DNA fragments were purified using the Qiagen MinElute kit, and subsequently PCR-amplified with the Nextera DNA sample kit using the following conditions: (1) 5 minutes at 72°C, (2) 1 minute at 98°C, (3) 15 seconds at 98°C, (4) 30 seconds at 63°C, (5) one minute at 72°C, (6) Go to step 3 eleven times, (7) hold at 10°C. All ATAC-seq libraries were sequenced on a Nextseq 500.