ChIP-Atlas: SRX997759

Antigen

Cell type Class: Neural
Cell type: Brain
MeSH Description: The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: ChIP experiments were performed as described (Feng et al. 2011) with minor changes. Mouse liver, brain (ventral tegmental area), and epididymal white adipose tissue (eWAT) were harvested, minced and cross-linked in 1% formaldehyde for 20min, followed by quenching with 1/20 volume of 2.5M glycine solution for 5 min, and two washes with 1×PBS. Nuclear extracts were prepared by Dounce homogenization in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC). Chromatin fragmentation was performed by sonication in lysis buffer (50mM Tris-HCL ph 8.0, 0.1%SDS, 10mM EDTA), using the Bioruptor (Diagenode). Proteins were immune-precipitated in ChIP buffer, and crosslinking was reversed overnight at 65°C in SDS buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS, pH 8), and DNA isolated using phenol/chloroform/isoamyl alcohol. DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina, using adaptor oligo and primers from Illumina, enzymes from New England Biolabs and PCR Purification Kit and MinElute Kit from Qiagen.