ChIP-Atlas: ERX161921

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.

ENA first public: 2013-07-12
ENA last update: 2018-03-08
ENA-CHECKLIST: ERC000011
External Id: SAMEA2161855
INSDC center alias: Cancer Research UK, Cambridge Research Institute, Robinson Way, Cambridge, UK
INSDC center name: Cancer Research UK, Cambridge Research Institute, Robinson Way, Cambridge, UK
INSDC first public: 2013-07-12T17:00:49Z
INSDC last update: 2018-03-08T16:37:00Z
INSDC status: public
Submitter Id: E-MTAB-1104_furthernewsamples:tc152038_brain
age: 2 to 6 month
broker name: ArrayExpress
common name: house mouse
developmental stage: adult
genotype: Tc1_with_hschr21
individual: tc152038
organism part: brain
sample name: E-MTAB-1104_furthernewsamples:tc152038_brain
sex: male

library_name: do1816_H3K4me3_brain_millipore_05-1339_tc1TC152038_CRI02
library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: doi:10.1016/j.ymeth.2009.03.001; Crosslinked animal livers were dounce homogenized into a single cell suspension and rinsed with ice cold PBS. Each pellet of cross-linked material was resuspended in 10 ml of LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100) and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4 C. Pellets were then rinsed in 10 ml of LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA) and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4 C. The nuclei preparation was resuspended in 3 ml LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin in the nuclei fraction was fragmented to an average length of 300 bp by sonication. After sonication 300 l of 10% Triton X-100 was added to the 3 ml of sonicated lysate and debris was removed by centrifugation at 20,000 x rcf for 10 minutes at 4 C.