title: GSM4290982: Normal_Rep1 93-11 HiC; Oryza sativa; Hi-C
library_construction_protocol: 2 g aerial parts of the rice seedlings were fixed with formaldehyde, and lysed and grounded into powder in liquid nitrogen. The procedure for the Hi-C experiment, including chromatin digestion, labelling of DNA ends, DNA ligation, purification and fragmentation, was as described previously (Xie et al., 2015). The cross-linked DNA were digested with Dpn II restriction enzyme by incubating overnight at 37 °C. DNA ends were labeled with biotin and incubated at 37 °C for 45 min, and the enzyme was inactivated with 20% SDS solution. DNA ligation as performed by the addition of T4 DNA ligase (Fermentas) and incubation at 4 °C for 1 h followed by 22 °C for 4 h. After ligation, proteinase K was added to reverse cross-linking during incubation at 65 °C overnight. DNA fragments were purified and dissolved in 86 µl of water. Unligated ends were then removed. Purified DNA was fragmented to a size of 300 - 700 bp using a sonicator (Covaris S220), and DNA ends were then repaired. DNA fragments labeled by biotin were finally separated on Streptavidin C1 beads (Life Technologies). Chimeric fragments representing the original cross-linked long-distance physical interactions were then processed into paired-end sequencing libraries. Hi-C libraries were constructed with an Illumina TruSeq DNA Sample Prep Kit and sequenced on an Illumina HiSeq X-ten platform (Illumina, USA) with 2 x 150-bp reads.
attributes.tag: GEO Accession
attributes.value: GSM4290982