title: GSM5104861: EV rep1 H3K4me3 h9coD35 SVA-KO; Homo sapiens; ChIP-Seq
library_construction_protocol: Organoids were rinsed in medium, homogonized in a 2ml Kontes Glass Co. dounce and immediately crosslinked after. Cells were lysed, chromatin was sheared to ~400bp fragments and chromatin was extracted using antibody-coated beads. DNA was purified using RNase cocktail enzyme mix, proteinase K, two phenol:chloroform (1:1) and one chloroform extractions followed by DNA precipitation in ethanol and a Zymo DNA Clean & Concentrator clean-up. TruSeq ChIP Library Preparation Kit (Illumina) with the following modifications: DNA clean & concentrator-5 kit (Zymo research) was used instead of beads for DNA purification. Size selections were performed before and after amplification on an E-gel Safe Imager (Invitrogen) using 2% E-gel SizeSelect gels (Invitrogen). The ChIP-DNA fraction of 300-400 bp in size (including adapters) was isolated and purified. ChIP-seq 75bp paired end reads on a NextSeq 550 device.