ChIP-Atlas: SRX685926

Antigen

Cell type Class: Neural
Cell type: Cerebral Cortex
MeSH Description: Type of cerebral cortex which does not pass through a perinatal phase of six-layered structure as in the NEOCORTEX and develops into three or four layers in the mature brain. Allocortex has three subareas: archi- paleo- and periallo-cortex.

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: Crosslinked material was sonicated with a Bioruptor (Diagenode) with 30 sec. on/off cycles to an average size range of 150-350bp as visualized by agarose gel electrophoresis. Sonicated supernatants were diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris pH 8.1, 167mM NaCl) before immunoprecipitation. 6uL antibody (anti-Zic 1/2 C-terminus, or total rabbit IgG, Millipore, Cat. #12-370) was first incubated with 100uL Dynabeads Protein G (Invitrogen) beads for 4 h. at 4°C, then the antibody conjugate was added to 6 mL of cell lysis for overnight IP. Standard TruSeq adapters were ligated for library preparation using the MicroPlex Library Preparation Kit (Diagenode). C57BL/6Ncrl male and female mice at P7 or P60 were deeply anesthetized with isofluorane and decapitated for brain harvesting. The cerebellar cortex was dissected, dounced in 1% formaldehyde PBS buffer, incubated at room temperature for 15 minutes, washed 2x with cold PBS, and then lysed in 600 uL lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1). We pooled cerebellum or cortex from three P7 mice or two P60 mice for each biological replicate.