Illumina HiSeq 4000 paired end sequencing; SPATIaL-seq of primary HepG2 cells
SPATIaL-seq of primary HepG2 cells
HepG2 cells were grown in DMEM + 10% FBS + 1% pen-strep media in 10cm dishes. HepG2 cells were harvested from the 10cm dish via trypsinization and counted.  10 million cells from triplicate plates were fixed. The initial 3C libraries were generated following a previously published protocol (Hughes et al., Nature genetics, 2014). The DNA was digested using DpnII, then re-ligated together using T4 DNA ligase, and finally isolated by phenol/chloroform extraction. The 3C libraries were sonicated to an average size of 300bp. Agilent SureSelect library capture protocol was then applied with capture probes targeting both ends of DpnII restriction fragments that overlap promoters of protein-coding, noncoding, antisense, snRNA, miRNA, snoRNA and lincRNA transcripts, totaling 36,691 RNA baited fragments. The bait list is provided in the file baits_1frag.bed.
Experimental Factor: replicate
biological replicate 1