title: GSM4115890: PFC_Setd1a_ChIPSeq_rep1; Mus musculus; ChIP-Seq
library_construction_protocol: Whole prefrontal cortex was dissected from 6-week old wild-type (WT) mice. Dissected tissue was thoroughly minced on ice using razor blades, then fixed with EGS for 30 min and/or for 5 min at room temperature with methanol-free formaldehyde (Pierce, Thermo Fisher Scientific) diluted to 1% in PBS. Fixation was quenched by adding 1/10th volume of 1.25 M glycine. Fixed tissue was collected by centrifugation at 200 g for 5 min at 4ºC, then washed twice with cold PBS. Washed tissue was flash-frozen with liquid nitrogen then cryofractured using a Covaris CryoPrep Impactor on power setting 6. Nuclei and chromatin immunoprecipitation were performed as in Markenscoff-Papadimitriou et al.(Markenscoff-Papadimitriou et al., 2014): briefly, the cryofractured tissue was lysed in ChIP Lysis Buffer (50 mM Tris-HCl pH 7.5, 150 nM NaCl, 0.5% NP-40, 0.25% Sodium Deoxychoalate, 0.1% SDS) in rotation for 40 min at 4ºC. Nuclei were centrifuged (1700x g, 5 min, 4ºC), and the pellet was resuspended in shearing buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8, 0.25% SDS), then sheared on a Covaris S2 sonicator (12 or 16  min, 2% Duty Cycle, Intensity 3, 200 cycles per burst, frequency sweeping). Sheared chromatin was centrifuged (10,000 g for 10 min at 4ºC) to remove insoluble material. Sheared chromatin was diluted 5-fold with ChIP Dilution Buffer (CDB: 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS) and pre-cleared for two hours at 4ºC with protein G dynabeads (Thermo Fisher Scientific). Each ChIP was set up with the appropriate antibody (10 mg of anti-Setd1a, 1 mg of anti-H3K27ac, -H3K4me2 and -H3K4me3, 3 mg of anti-H3K4me1, 5 mg of Mef2) and 10-20 mg of cleared chromatin, incubating then overnight at 4ºC. Protein G dynabeads were blocked overnight with 2 mg/ml yeast tRNA (Thermo Fisher Scientific), then added to antibody bound chromatin and rotated for 3 hr at 4ºC. Bead-bound chromatin was washed 5 times with LiCl Wash Buffer (100 mM Tris-HCl pH 7.5, 500 mM LiCl, 1% NP-40, 1% Sodium Deoxycholate) and once with TE (pH7.5). DNA was eluted from beads by incubating at 65ºC for 30 min with 25 mL ChIP Elution Buffer (1% SDS, 0.1 M Sodium Bicarbonate). This elution was repeated and the combined elution fractions were incubated overnight at 65ºC with proteinase K (Thermo Fisher Scientific) and RNaseA (Thermo Fisher Scientific). ChIP DNA was purified 1.8X of AMPure XP beads and eluted in 30 ml of nuclease free water. Libraries were prepared with Ovation Ultralow System V2 1-16 (NuGEN technologies) according to manufacturers' recommendation.
attributes.tag: GEO Accession
attributes.value: GSM4115890