ChIP-Atlas: SRX5842786

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: After isolation of nucleus with lysis buffer (50 mM HEPES-KOH, 135 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% TritonX100), the chromatin was digested with micrococcal nuclease. The pellet was resuspended with IP buffer (50 mM Tris-HCl, 100 mM NaCl, 10 mM EDTA, 0.1% SDS, and 1% TritonX100) and the nuclear membrane was broken with sonication. IP was performed with respective antibody overnight at cold room. The antibody-antigen was precipitated with magnetic beads. The ChIPed DNA was eluted and extracted with DNA extraction kit (MN #740609.250). Libraries were made using KAPA Hyper Prep kit (KAPABiosystems #KR0961) following manufacturer's instructions. Briefly, 30 ng from each immunoprecipitated or Input DNA, were end-repaired, phosphorylated, A-tailed and ligated to adaptors (Roche SeqCap Adapter kit A #07141530001). Ligated products were size selected with 0.8X SPRI beads to obtain 250~350 bp of DNA. After purification, 8-cycle PCR amplification reaction was performed. PCR product was cleaned by the use of 1X SPRI beads. Final product was resuspended in 30 ul of Tris buffer.