GSM3934950: YueLab-H3K4me3-embryonic-Brain-rep1; Danio rerio; ChIP-Seq
Zebrafish embryonic tissue ChIP-seq was performed similarly to the adult tissue with a few modifications. For embryonic trunk, 50 trunks of 1 dpf embryos were dissected and digested in 500 µL of 0.25% trypsin at room temperature for 20 min. The reaction was then neutralized with FBS.  Trunk cells were washed once with cold 1X PBS and cross-linked with 1% formaldehyde at room temperature for 12 min. For embryonic neuronal cells, Tg(Huc:Kaede) transgenic fish were crossed with wildtype Tuebingen fish. At 1 dpf, embryos were checked under the fluorescence microscope and green positive embryos were selected, dechorionated and pipetted in calcium free Ringer's solution to remove yolk. Supernatant was removed and 500 µL of 0.25% trypsin was added to digeste embryos at room temperature for 20 min. Neutralized with 500 µL of FBS and washed once with cold 1X PBS, digested cells were then cross-linked with 1% formaldehyde at room temperature for 12 min. Cells were then sorted and only green fluoresced cells, which corresponded to embryonic neuronal cells, were collected . To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit's protocol, added A using Klenow  fragment (3'->5' exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp.