title: GSM1148637: E14Tg2a_Input_DNA; Mus musculus; ChIP-Seq
library_construction_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K56ac antibody. Chromatin immunoprecipitation (ChIP) was performed using about 20 milloin cells with the following protocol described earlier. Briefly, E14Tg2a cells were cross linked with formaldehyde for 10 minutes, lysed in 10mM Tris-EDTA pH 8.0 with 1% SDS, and sonicated (Fisher Scientific #550 Sonic Dismembrator) on ice 4 times at 15 second pulses interrupted by 45 second pauses on power 4 followed by 2 times at 20 seconds pulses interrupted by 40 seconds pauses on power 2. Clarified sheared chromatin was immunoprecipitated with antibodies to histone H3K56ac (generated by Michael Grunstein's lab) overnight at 4°C. Immunoprecipitated DNA was collected with protein A dynabeads for 3 hours, washed twice for 5 minutes at 4°C with wash buffers and eluted with 1% SDS. Eluates were heated at 65°C to reverse crosslinks, treated with RNase and proteinase K, and DNA was purified with the Qiagen PCR purification kit. 10ng DNA was amplified using the ChIPSeq DNA Sample Prep. Kit (Illumina, P/N # 1003473), and sequenced with Illumina Genome Analyzer Hiseq2000 at the UCLA Broad Stem Cell Research Center high throughput sequencing facility.