title: GSM2334832: Hi-C RPMI-8226 HindIII; Homo sapiens; OTHER
library_construction_protocol: Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer. Cross-linked DNA was digested with HindIII, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. Other steps were following in-situ Hi-C protocol (Rao et al., 2014, Cell). Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
attributes.tag: GEO Accession
attributes.value: GSM2334832