ChIP-Atlas: SRX445333

Antigen

Cell type Class: Neural
Cell type: Nucleus Accumbens
MeSH Description: Collection of pleomorphic cells in the caudal part of the anterior horn of the LATERAL VENTRICLE, in the region of the OLFACTORY TUBERCLE, lying between the head of the CAUDATE NUCLEUS and the ANTERIOR PERFORATED SUBSTANCE. It is part of the so-called VENTRAL STRIATUM, a composite structure considered part of the BASAL GANGLIA.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: For each ChIP-seq replicate, bilateral 14-gauge NAc punches were pooled from 10 mice. Tissue was lightly fixed to cross-link DNA with associated proteins, and the material was further sheared (ACF1 and SNF2H) or MNase digested (histone H3) and immunoprecipitated using sheep anti-rabbit magnetic beads (Invitrogen) conjugated to an antibody that specifically recognizes ACF1 (Bethyl), SNF2H, or H3 (Abcam). Immunoprecipitated DNA and total (input) genomic DNA were prepared for ChIP-seq using an Illumina kit according to the manufacturer’s instructions. Each experimental condition was analyzed with independent biological triplicates. Briefly, each sample underwent end repair followed by addition of an A base to the 3′ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 2% agarose gel. The range of excision was 200–300 bp. After DNA clean up, samples were amplified with 15 (H3) or 19 (ACF1 and SNF2H) cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. The resulting libraries were sequenced on an Illumina HiSeq 2500 with 100 bp read length.