title: Epigenetic comparison of human DNA in specific human tissues to human DNA in transgenic mouse tissues
design: Epigenetic comparison of human DNA in specific human tissues to human DNA in transgenic mouse tissues
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.
attributes.tag: Experimental Factor: organism
attributes.value: Mus musculus
attributes.tag: Experimental Factor: genotype
attributes.value: Tc1_with_hschr21
attributes.tag: Experimental Factor: immunoprecipitate
attributes.value: H3K4me3
attributes.tag: Experimental Factor: organism part
attributes.value: spleen
attributes.tag: Experimental Factor: sex
attributes.value: male