ChIP-Atlas: SRX5620752

Antigen

Cell type Class: Neural
Cell type: Corpus Striatum
MeSH Description: Striped GRAY MATTER and WHITE MATTER consisting of the NEOSTRIATUM and paleostriatum (GLOBUS PALLIDUS). It is located in front of and lateral to the THALAMUS in each cerebral hemisphere. The gray substance is made up of the CAUDATE NUCLEUS and the lentiform nucleus (the latter consisting of the GLOBUS PALLIDUS and PUTAMEN). The WHITE MATTER is the INTERNAL CAPSULE.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Compound- or vehicle-treated cells were crosslinked with 1% formaldehyde for 8 minutes and quenched with glycine for 5 minutes, lysed in 2X lysis buffer (50mM Tris-HCl pH8, 150mM NaCl, 1% Triton X-100, 0.1% Na Deoxycholate, 5mM CaCl2 and protease inhibitors) for 20 minutes on ice, and digested with 100u MNase (New England Biolabs M0247) for 10 minutes at 37°C. The MNase digestion was terminated by addition of 10mM EDTA. Chromatin was incubated with the anti-H3K4me3 antibody (Millipore 07-473, RRID: AB_1977252) overnight at 4°C, followed by incubation with Protein G beads (Invitrogen 10004D) for 2 hours at 4°C. The beads were washed with PBS (6x) and samples were eluted in EB (10mM Tris-HCl pH8, 5mM EDTA, 300mM NaCl, 0.1% SDS) supplemented with Proteinase K (New England Biolabs P8107S). SPRI beads were used for clean-up and yield was measured using Qubit Fluorimeter. Libraries were prepared using NEBNExt® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs E7645S). Libraries were sequenced on an Illumina Hi-Seq 2000 for single-end 50bp reads.