ChIP-Atlas: SRX3331740

Antigen

Cell type Class: Neural
Cell type: Prefrontal Cortex
MeSH Description: The rostral part of the frontal lobe, bounded by the inferior precentral fissure in humans, which receives projection fibers from the MEDIODORSAL NUCLEUS OF THE THALAMUS. The prefrontal cortex receives afferent fibers from numerous structures of the DIENCEPHALON; MESENCEPHALON; and LIMBIC SYSTEM as well as cortical afferents of visual, auditory, and somatic origin.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Mouse prefrontal cortex were dissected from the brain. Genomic DNAs were isolated by different brain tissues in 600 μl digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl), Proteinase K (Thermo) treatment at 55°C for overnight. The second day, 600 μl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (P-3803, Sigma) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer solution was transferred into a new Eppendorf tube and precipitated with 600 μl isopropanol. The pellet was washed with 75% ethanol, air-dried, and eluted with Nuclease-Free Water (Ambion). RNA was then reverse transcribed using a SuperScript® III First-Strand Synthesis System (Invitrogen). DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25–50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocol.