title: GSM7516891: HiChIP H3K4me3 neural retina, biological replicate 2; Homo sapiens; OTHER
library_construction_protocol: Post-mortem human neural retina and RPE/choroid mixtures were obtained through the Tissue Bank of Ghent University Hospital and Antwerp University Hospital under ethical approval of the Ethics Committee of Ghent University (2018/1072, B670201837286). Eye globes were provided with a description of time and cause of death, post-mortem circulation time, age and sex. None of the 6 donors had a prior known ophthalmological condition.  The eye globes were dissected on ice, followed by extraction of the neural retina and the retinal pigment epithelium/choroid. The resulting tissues were resuspended in 1XPBS supplemented with 10% Fetal Bovine Serum. The samples were processed according to Matelot & Noordermeer (2016) and cross-linking of nuclei was performed using 2% formaldehyde. Finally, the obtained nucleai were aliquoted per 10 million and snap frozen after supernatant removal. Samples were stored at -80°C. Extracted nuclei were processed for HiChIP preparation as previously described (Mumbach et al. 2016). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. Chromatin was sonicated in a Covaris M220 sonicator for fragments around 300 bp and immunoprecipitated with anti-H3K4me3 (abcam). DNA was extracted after cross-link reversal and biotinylated products were recovered with streptavidin-coated beads, TAGmented with Tn5 transposase and purified for library preparation. Preparation of HiChIP libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015