GSM6798160: Crypts, EPR cKO, 43A; Mus musculus; Hi-C
chromatin from crypts was crosslinked and digested using a restriction enzyme cocktail. The 5'-overhangs are then filled in, causing the digested ends to be labeled with a biotinylated nucleotide. Next, spatially proximal digested ends of DNA are ligated, capturing the sequence and structure of the genome. The ligated DNA is then purified, producing pure proximally-ligated DNA. The proximally-ligated DNA is then fragmented, and the biotinylated fragments are enriched. The enriched fragments are then subjected to a custom library preparation protocol utilizing the Arima Library Prep Module . Following Library prep we perform shallow sequencing (500k-2M paired-end reads) to assess the libraries' quality in terms of library complexity and long-range interaction information prior to proceeding with the capture. Once Hi-C is complete, the sample is pre-cleared to remove carry over biotinylated Hi-C molecules. The interactions of interest are then enriched using biotinylated RNA probes from the Arima Mouse Promoter Panel paired-end