ChIP Input: Crx-/- retina
Chromatin immunoprecipitation (ChIP) assay was performed as previously described.[Tran et al., 2014b] In summary, 6 pooled P14 C57BL/6J Wild type, or Crx-/-¾mouse retinas per sample were dissected and chromatin was cross-linked with 1% formaldehyde in PBS for 10 minute at room temperature. Crosslinked cells were lysed and fragmented by sonication. Chromatin fragments were immunoprecipitated with the Histone H3 (acetyl K27 - ab4729) (Abcam, Cambridge, UK) and trimethyl-Histone H3 (Lys4) (Millipore, 07-473) antibodies,¾or normal rabbit / mouse IgG (Santa Cruz Biotechnology, Dallas, TX) bound to Protein A beads (Millipore, 16-125), or A/G beads (Santa Cruz Biotechnology). After extensive washing, the immunoprecipitated chromatin was eluted, heated to 67çC to reverse the cross-links, and the DNA purified by ethanol precipitation. Libraries were prepared using the DNA SMART ChIP-Seq Kit (Clonetech, Mountain View, CA). 10ng of ChIP DNA was used as input for each sample.